1
|
Schnarr L, Olsson O, Kümmerer K. Biodegradation of flavonoids - Influences of structural features. CHEMOSPHERE 2024; 359:142234. [PMID: 38705418 DOI: 10.1016/j.chemosphere.2024.142234] [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: 12/14/2023] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Flavonoids, a class of natural products with a variety of applications in nutrition, pharmacy and as biopesticides, could substitute more harmful synthetic chemicals that persist in the environment. To gain a better understanding of the biodegradability of flavonoids and the influence of structural features, firstly, the ultimate biodegradation of 19 flavonoids was investigated with the Closed Bottle Test according to the OECD guideline 301 D. Secondly, regarding the fast abiotic degradation reported for several flavonoids with severe concentration decrease within hours and its possible impacts on the processes behind the ultimate biodegradation, primary degradation of 4 selected flavonoids was compared at conditions representing biodegradation, abiotic degradation, and mixed substrates by monitoring the flavonoids' concentrations with HPLC-UV/vis. Our results showed that 17 out of the 19 tested flavonoids were readily biodegradable. Structural features like a hydroxy group at C3, the C2-C3 bond order, a methoxy group in the B ring, and the position of the B ring in regard to the chromene core did not affect biodegradation of the tested flavonoids. Only flavone without any hydroxy groups and morin with an uncommon 2',4' pattern of hydroxy groups were non-readily biodegradable. Monitoring the concentration of 4 selected flavonoids by HPLC-UV/vis revealed that biodegradation occurred faster than abiotic degradation at CBT conditions with no other carbon sources present. The presence of an alternative carbon source tends to increase lag phases and decrease biodegradation rates. At this condition, abiotic degradation contributed to the degradation of unstable flavonoids. Overall, as a first tier to assess the environmental fate, our results indicate low risks for persistence of most flavonoids. Thus, flavonoids could represent benign substitutes for persistent synthetic chemicals.
Collapse
Affiliation(s)
- Lena Schnarr
- Institute of Sustainable Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany.
| | - Oliver Olsson
- Institute of Sustainable Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany.
| | - Klaus Kümmerer
- Institute of Sustainable Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany; Research and Education, International Sustainable Chemistry Collaborative Centre (ISC3), Universitätsallee 1, 21335, Lüneburg, Germany.
| |
Collapse
|
2
|
McGivern BB, Cronin DR, Ellenbogen JB, Borton MA, Knutson EL, Freire-Zapata V, Bouranis JA, Bernhardt L, Hernandez AI, Flynn RM, Woyda R, Cory AB, Wilson RM, Chanton JP, Woodcroft BJ, Ernakovich JG, Tfaily MM, Sullivan MB, Tyson GW, Rich VI, Hagerman AE, Wrighton KC. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nat Microbiol 2024; 9:1454-1466. [PMID: 38806673 PMCID: PMC11153144 DOI: 10.1038/s41564-024-01691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/02/2024] [Indexed: 05/30/2024]
Abstract
With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch. To inventory alternative polyphenol removal strategies, we built CAMPER, a gene annotation tool leveraging polyphenol enzyme knowledge gleaned across microbial ecosystems. Applying CAMPER to genome-resolved metatranscriptomes, we identified genes for diverse polyphenol-active enzymes expressed by various microbial lineages under a range of redox conditions. This shifts the paradigm that polyphenols stabilize carbon in saturated soils and highlights the need to consider both oxic and anoxic polyphenol metabolisms to understand carbon cycling in changing ecosystems.
Collapse
Affiliation(s)
- Bridget B McGivern
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Dylan R Cronin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Jared B Ellenbogen
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Mikayla A Borton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Eleanor L Knutson
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | | | - John A Bouranis
- Department of Environmental Science; University of Arizona, Tucson, AZ, USA
| | - Lukas Bernhardt
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Alma I Hernandez
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Rory M Flynn
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Reed Woyda
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Alexandra B Cory
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA
| | - Rachel M Wilson
- Department of Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Jeffrey P Chanton
- Department of Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jessica G Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Malak M Tfaily
- Department of Environmental Science; University of Arizona, Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Ann E Hagerman
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
3
|
Aoki N, Shimasaki T, Yazaki W, Sato T, Nakayasu M, Ando A, Kishino S, Ogawa J, Masuda S, Shibata A, Shirasu K, Yazaki K, Sugiyama A. An isoflavone catabolism gene cluster underlying interkingdom interactions in the soybean rhizosphere. ISME COMMUNICATIONS 2024; 4:ycae052. [PMID: 38707841 PMCID: PMC11069340 DOI: 10.1093/ismeco/ycae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/19/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Plant roots secrete various metabolites, including plant specialized metabolites, into the rhizosphere, and shape the rhizosphere microbiome, which is crucial for the plant health and growth. Isoflavones are major plant specialized metabolites found in legume plants, and are involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. However, it remains largely unknown the molecular basis underlying the isoflavone-mediated interkingdom interactions in the legume rhizosphere. Here, we isolated Variovorax sp. strain V35, a member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation named ifc. The characterization of ifc mutants and heterologously expressed Ifc enzymes revealed that isoflavones undergo oxidative catabolism, which is different from the reductive metabolic pathways observed in gut microbiota. We further demonstrated that the ifc genes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to the detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an isoflavone catabolism gene cluster in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume-microbiota interactions.
Collapse
Affiliation(s)
- Noritaka Aoki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohisa Shimasaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Wataru Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoaki Sato
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akinori Ando
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigenobu Kishino
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
4
|
Rogowska-van der Molen MA, Berasategui-Lopez A, Coolen S, Jansen RS, Welte CU. Microbial degradation of plant toxins. Environ Microbiol 2023; 25:2988-3010. [PMID: 37718389 DOI: 10.1111/1462-2920.16507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.
Collapse
Affiliation(s)
- Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Aileen Berasategui-Lopez
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Amsterdam Institute for Life and Environment, Section Ecology and Evolution, Vrije Universiteit, Amsterdam, The Netherlands
| | - Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| |
Collapse
|
5
|
Rymbai LD, Klausmeyer KK, Farmer PJ. The case for an oxidopyrylium intermediate in the mechanism of quercetin dioxygenases. J Inorg Biochem 2023; 247:112343. [PMID: 37549474 DOI: 10.1016/j.jinorgbio.2023.112343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
The quercetin dioxygenases (QDOs) are unusual metalloenzymes in that they display ring-opening dioxygenase activity with several different first-row transition metal ions which do not undergo redox changes during turnover. The QDOs are also unique in that the substrate binds as an η1-flavonolate rather than the η2 -bidentate mode seen in all reported model complexes. The flavonol substrates were early examples of excited state intramolecular proton transfer (ESIPT) phenomena, in which photoexcitation causes an H-atom exchange between the adjacent hydroxyl and ketone, generating an oxidopyrylium emissive state. These oxidopyryliums undergo ring-opening dioxygenations analogous to the enzymatic reactions. Our hypothesis is that lability of the divalent metal ion may allow access to a reactive oxidopyrylium intermediate via coordination switching from the oxy to ketone position, which allows reaction with O2. In this report, we use a straight-forward methylation strategy to generate a panel of flavonol and thioflavonol derivatives modeling several η1- and η2-coordination modes. Methylation of 3-hydroxythioflavone generates an air stable η1 hydroxopyrylium salt, which undergoes rapid ring-opening dioxygenation by deprotonation or photoexcitation. By comparison, the η1-methoxyflavonol does not react with O2 under any condition. We find that any of the studied flavonol derivatives, η1 or η2, which demonstrates ESIPT-like oxidopyrylium emissions undergo QDO-like ring-opening reactions with dioxygen. The implications of these results concerning the mechanism of QDOs and related dioxygenases is discussed.
Collapse
Affiliation(s)
- Lasien D Rymbai
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States of America
| | - Kevin K Klausmeyer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States of America
| | - Patrick J Farmer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States of America.
| |
Collapse
|
6
|
Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
Collapse
Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
| |
Collapse
|
7
|
Wang L, Chen M, Lam PY, Dini-Andreote F, Dai L, Wei Z. Multifaceted roles of flavonoids mediating plant-microbe interactions. MICROBIOME 2022; 10:233. [PMID: 36527160 PMCID: PMC9756786 DOI: 10.1186/s40168-022-01420-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 11/09/2022] [Indexed: 05/07/2023]
Abstract
Plant-microbe interactions dynamically affect plant growth, health, and development. The mechanisms underpinning these associations are-to a large extent-mediated by specialized host-derived secondary metabolites. Flavonoids are one of the most studied classes of such metabolites, regulating both plant development and the interaction with commensal microbes. Here, we provide a comprehensive review of the multiple roles of flavonoids in mediating plant-microbe interactions. First, we briefly summarize the general aspects of flavonoid synthesis, transport, and exudation in plants. Then, we review the importance of flavonoids regulating plant-microbe interactions and dynamically influencing the overall community assembly of plant-root microbiomes. Last, we highlight potential knowledge gaps in our understanding of how flavonoids determine the interactions between plants and commensal microbes. Collectively, we advocate the importance of advancing research in this area toward innovative strategies to effectively manipulate plant-microbiome composition, in this case, via flavonoid production and exudation in plant roots. Video Abstract.
Collapse
Affiliation(s)
- Lanxiang Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Moxian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Pui-Ying Lam
- Center for Crossover Education, Graduate School of Engineering Science, Akita University, Tegata Gakuen-machi 1-1, Akita City, Akita, 010-8502, Japan
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
8
|
Structure-based molecular characterization of the YetL transcription factor from Bacillus subtilis. Biochem Biophys Res Commun 2022; 607:146-151. [DOI: 10.1016/j.bbrc.2022.03.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/22/2022]
|
9
|
Sugiyama A. Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture. Biosci Biotechnol Biochem 2021; 85:1919-1931. [PMID: 34113972 DOI: 10.1093/bbb/zbab106] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/04/2021] [Indexed: 01/13/2023]
Abstract
Plants are in constant interaction with a myriad of soil microorganisms in the rhizosphere, an area of soil in close contact with plant roots. Recent research has highlighted the importance of plant-specialized metabolites (PSMs) in shaping and modulating the rhizosphere microbiota; however, the molecular mechanisms underlying the establishment and function of the microbiota mostly remain unaddressed. Flavonoids and saponins are a group of PSMs whose biosynthetic pathways have largely been revealed. Although these PSMs are abundantly secreted into the rhizosphere and exert various functions, the secretion mechanisms have not been clarified. This review summarizes the roles of flavonoids and saponins in the rhizosphere with a special focus on interactions between plants and the rhizosphere microbiota. Furthermore, this review introduces recent advancements in the dynamics of these metabolites in the rhizosphere and indicates potential applications of PSMs for crop production and discusses perspectives in this emerging research field.
Collapse
Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| |
Collapse
|
10
|
Boronat A, Rodriguez-Morató J, Serreli G, Fitó M, Tyndale RF, Deiana M, de la Torre R. Contribution of Biotransformations Carried Out by the Microbiota, Drug-Metabolizing Enzymes, and Transport Proteins to the Biological Activities of Phytochemicals Found in the Diet. Adv Nutr 2021; 12:2172-2189. [PMID: 34388248 PMCID: PMC8634308 DOI: 10.1093/advances/nmab085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/17/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022] Open
Abstract
The consumption of dietary phytochemicals has been associated with several health benefits and relevant biological activities. It is postulated that biotransformations of these compounds regulated by the microbiota, Phase I/II reactions, transport proteins, and deconjugating enzymes contribute not only to their metabolic clearance but also, in some cases, to their bioactivation. A number of factors (age, genetics, sex, physiopathological conditions, and the interplay with other dietary phytochemicals) modulating metabolic activities are important sources and contributors to the interindividual variability observed in clinical studies evaluating the biological activities of phytochemicals. In this review, we discuss all the processes that can affect the bioaccessibility and beneficial effects of these bioactive compounds. Herein, we argue that the role of these factors must be further studied to correctly understand and predict the effects observed following the intake of phytochemicals. This is, in particular, with regard to in vitro investigations, which have shown great inconsistency with preclinical and clinical studies. The complexity of in vivo metabolic activity and biotransformation should therefore be considered in the interpretation of results in vitro and their translation to human physiopathology.
Collapse
Affiliation(s)
- Anna Boronat
- Integrative Pharmacology and Systems Neurosciences Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jose Rodriguez-Morató
- Integrative Pharmacology and Systems Neurosciences Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain,Physiopathology of Obesity and Nutrition Networking Biomedical Research Centre (CIBEROBN), Madrid, Spain,Department of Experimental and Health Sciences (UPF-CEXS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gabriele Serreli
- Department of Biomedical Science, Pathology Section, Experimental Pathology Unit, University of Cagliari, Montserrato, Italy
| | - Montserrat Fitó
- Physiopathology of Obesity and Nutrition Networking Biomedical Research Centre (CIBEROBN), Madrid, Spain,Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute (CAMH), Toronto, Canada,Department of Pharmacology, Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Monica Deiana
- Department of Biomedical Science, Pathology Section, Experimental Pathology Unit, University of Cagliari, Montserrato, Italy
| | | |
Collapse
|
11
|
Screening of Human Gut Bacterial Culture Collection Identifies Species That Biotransform Quercetin into Metabolites with Anticancer Properties. Int J Mol Sci 2021; 22:ijms22137045. [PMID: 34208885 PMCID: PMC8269047 DOI: 10.3390/ijms22137045] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
We previously demonstrated that flavonoid metabolites inhibit cancer cell proliferation through both CDK-dependent and -independent mechanisms. The existing evidence suggests that gut microbiota is capable of flavonoid biotransformation to generate bioactive metabolites including 2,4,6-trihydroxybenzoic acid (2,4,6-THBA), 3,4-dihydroxybenzoic acid (3,4-DHBA), 3,4,5-trihyroxybenzoic acid (3,4,5-THBA) and 3,4-dihydroxyphenylacetic acid (DOPAC). In this study, we screened 94 human gut bacterial species for their ability to biotransform flavonoid quercetin into different metabolites. We demonstrated that five of these species were able to degrade quercetin including Bacillus glycinifermentans, Flavonifractor plautii, Bacteroides eggerthii, Olsenella scatoligenes and Eubacterium eligens. Additional studies showed that B. glycinifermentans could generate 2,4,6-THBA and 3,4-DHBA from quercetin while F. plautii generates DOPAC. In addition to the differences in the metabolites produced, we also observed that the kinetics of quercetin degradation was different between B. glycinifermentans and F. plautii, suggesting that the pathways of degradation are likely different between these strains. Similar to the antiproliferative effects of 2,4,6-THBA and 3,4-DHBA demonstrated previously, DOPAC also inhibited colony formation ex vivo in the HCT-116 colon cancer cell line. Consistent with this, the bacterial culture supernatant of F. plautii also inhibited colony formation in this cell line. Thus, as F. plautii and B. glycinifermentans generate metabolites possessing antiproliferative activity, we suggest that these strains have the potential to be developed into probiotics to improve human gut health.
Collapse
|
12
|
Soboleva T, Berreau LM. 3-Hydroxyflavones and 3-Hydroxy-4-oxoquinolines as Carbon Monoxide-Releasing Molecules. Molecules 2019; 24:E1252. [PMID: 30935018 PMCID: PMC6479552 DOI: 10.3390/molecules24071252] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/26/2022] Open
Abstract
Carbon monoxide-releasing molecules (CORMs) that enable the delivery of controlled amounts of CO are of strong current interest for applications in biological systems. In this review, we examine the various conditions under which CO is released from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines to advance the understanding of how these molecules, or derivatives thereof, may be developed as CORMs. Enzymatic pathways from quercetin dioxygenases and 3-hydroxy-4-oxoquinoline dioxygenases leading to CO release are examined, along with model systems for these enzymes. Base-catalyzed and non-redox-metal promoted CO release, as well as UV and visible light-driven CO release from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines, are summarized. The visible light-induced CO release reactivity of recently developed extended 3-hydroxyflavones and a 3-hydroxybenzo[g]quinolone, and their uses as intracellular CORMs, are discussed. Overall, this review provides insight into the chemical factors that affect the thermal and photochemical dioxygenase-type CO release reactions of these heterocyclic compounds.
Collapse
Affiliation(s)
- Tatiana Soboleva
- Department of Chemistry & Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322-0300, USA.
| | - Lisa M Berreau
- Department of Chemistry & Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322-0300, USA.
| |
Collapse
|
13
|
Zheng C, Guo S, Tennant WG, Pradhan PK, Black KA, Dos Santos PC. The Thioredoxin System Reduces Protein Persulfide Intermediates Formed during the Synthesis of Thio-Cofactors in Bacillus subtilis. Biochemistry 2019; 58:1892-1904. [PMID: 30855939 DOI: 10.1021/acs.biochem.9b00045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthesis of Fe-S clusters and other thio-cofactors requires the participation of redox agents. A shared feature in these pathways is the formation of transient protein persulfides, which are susceptible to reduction by artificial reducing agents commonly used in reactions in vitro. These agents modulate the reactivity and catalytic efficiency of biosynthetic reactions and, in some cases, skew the enzymes' kinetic behavior, bypassing sulfur acceptors known to be critical for the functionality of these pathways in vivo. Here, we provide kinetic evidence for the selective reactivity of the Bacillus subtilis Trx (thioredoxin) system toward protein-bound persulfide intermediates. Our results demonstrate that the redox flux of the Trx system modulates the rate of sulfide production in cysteine desulfurase assays. Likewise, the activity of the Trx system is dependent on the rate of persulfide formation, suggesting the occurrence of coupled reaction schemes between both enzymatic systems in vitro. Inactivation of TrxA (thioredoxin) or TrxR (thioredoxin reductase) impairs the activity of Fe-S enzymes in B. subtilis, indicating the involvement of the Trx system in Fe-S cluster metabolism. Surprisingly, biochemical characterization of TrxA reveals that this enzyme is able to coordinate Fe-S species, resulting in the loss of its reductase activity. The inactivation of TrxA through the coordination of a labile cluster, combined with its proposed role as a physiological reducing agent in sulfur transfer pathways, suggests a model for redox regulation. These findings provide a potential link between redox regulation and Fe-S metabolism.
Collapse
Affiliation(s)
- Chenkang Zheng
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Selina Guo
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - William G Tennant
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Pradyumna K Pradhan
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States.,Department of Chemistry and Biochemistry , The University of North Carolina at Greensboro , Greensboro , North Carolina 27412 , United States
| | - Katherine A Black
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States.,Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Patricia C Dos Santos
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| |
Collapse
|
14
|
Kawabata K, Yoshioka Y, Terao J. Role of Intestinal Microbiota in the Bioavailability and Physiological Functions of Dietary Polyphenols. Molecules 2019; 24:E370. [PMID: 30669635 PMCID: PMC6359708 DOI: 10.3390/molecules24020370] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 12/29/2022] Open
Abstract
Polyphenols are categorized as plant secondary metabolites, and they have attracted much attention in relation to human health and the prevention of chronic diseases. In recent years, a considerable number of studies have been published concerning their physiological function in the digestive tract, such as their prebiotic properties and their modification of intestinal microbiota. It has also been suggested that several hydrolyzed and/or fission products, derived from the catabolism of polyphenols by intestinal bacteria, exert their physiological functions in target sites after transportation into the body. Thus, this review article focuses on the role of intestinal microbiota in the bioavailability and physiological function of dietary polyphenols. Monomeric polyphenols, such as flavonoids and oligomeric polyphenols, such as proanthocyanidins, are usually catabolized to chain fission products by intestinal bacteria in the colon. Gallic acid and ellagic acid derived from the hydrolysis of gallotannin, and ellagitannin are also subjected to intestinal catabolism. These catabolites may play a large role in the physiological functions of dietary polyphenols. They may also affect the microbiome, resulting in health promotion by the activation of short chain fatty acids (SCFA) excretion and intestinal immune function. The intestinal microbiota is a key factor in mediating the physiological functions of dietary polyphenols.
Collapse
Affiliation(s)
- Kyuichi Kawabata
- Faculty of Clinical Nutrition and Dietetics, Konan Women's University, 6-2-23 Morikita-machi, Higashinada-ku, Kobe City, Hyogo 658-0001, Japan.
| | - Yasukiyo Yoshioka
- Faculty of Clinical Nutrition and Dietetics, Konan Women's University, 6-2-23 Morikita-machi, Higashinada-ku, Kobe City, Hyogo 658-0001, Japan.
| | - Junji Terao
- Faculty of Clinical Nutrition and Dietetics, Konan Women's University, 6-2-23 Morikita-machi, Higashinada-ku, Kobe City, Hyogo 658-0001, Japan.
| |
Collapse
|
15
|
Draft Genome Sequence of Plant Growth-Promoting Bacillus altitudinis Strain PAE4. Microbiol Resour Announc 2018; 7:MRA00962-18. [PMID: 30533694 PMCID: PMC6256563 DOI: 10.1128/mra.00962-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 11/20/2022] Open
Abstract
We report here the draft genome of Bacillus altitudinis strain PAE4, a thermophilic plant growth-promoting rhizobacterium isolated from the coastal ridge of the Mediterranean Sea in Egypt. Besides heat shock protein genes, several genes encoding phytobeneficial properties were identified.
Collapse
|
16
|
Li H, Wang X, Tian G, Liu Y. Insights into the dioxygen activation and catalytic mechanism of the nickel-containing quercetinase. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00187a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic mechanism of Ni-QueDFLA was elucidated by QM/MM calculations, and the different reactivities of nickel and iron were illuminated.
Collapse
Affiliation(s)
- Hong Li
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Ge Tian
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| |
Collapse
|
17
|
Sun YJ, Huang QQ, Zhang JJ. Set of Fe(II)-3-Hydroxyflavonolate Enzyme-Substrate Model Complexes of Atypically Coordinated Mononuclear Non-Heme Fe(II)-Dependent Quercetin 2,4-Dioxygenase. ACS OMEGA 2017; 2:5850-5860. [PMID: 31457842 PMCID: PMC6644611 DOI: 10.1021/acsomega.7b00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/31/2017] [Indexed: 06/10/2023]
Abstract
With the aim of revealing the catalytic role of atypically coordinated (3His-1Glu) active site mononuclear non-heme Fe(II)-dependent quercetin 2,4-dioxygenase (Fe-2,4-QD) and the electronic effects of the model ligands on the reactivity toward dioxygen, a set of p/m-R-substituted carboxylate-containing ligand-supported Fe(II)-3-hydroxyflavonolate complexes, [FeIILR(fla)] (LRH: 2-{[bis(pyridin-2-ylmethyl)amino]methyl}-p/m-R-benzoic acid; R: p-OMe (1), p-Me (2), m-Br (4), and m-NO2 (5); fla: 3-hydroxyflavonolate), were synthesized and characterized as structural and functional models for the ES (enzyme-substrate) complexes of Fe-2,4-QD. [FeIILR(fla)] show relatively high enzyme-type reactivity (dioxygenative ring opening of the coordinated substrate fla, single-turnover reaction) at low temperatures (30-65 °C). The reaction shows a linear Hammett plot (ρ = -1.21), and electron donating groups enhance the reaction rates. The notable difference on the reactivity can be rationalized from the electronic nature of the substituent in the ligands, which could tune the reactivity via tuning Lewis acidity of the Fe(II) ion, electron density, and the redox potential of fla. The properties and the reactivity show approximately linear correlations between λmax or E 1/2 of fla and the reaction rate constant k. This work sheds light not only on understanding of electronic effects of the ligands and the property-reactivity relationship but also on the role of the catalytic reaction by Fe-2,4-QD.
Collapse
|
18
|
Raie DS, Mhatre E, Thiele M, Labena A, El-Ghannam G, Farahat LA, Youssef T, Fritzsche W, Kovács ÁT. Application of quercetin and its bio-inspired nanoparticles as anti-adhesive agents against Bacillus subtilis attachment to surface. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 70:753-762. [DOI: 10.1016/j.msec.2016.09.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/15/2016] [Accepted: 09/19/2016] [Indexed: 11/28/2022]
|
19
|
Stevens JF, Maier CS. The Chemistry of Gut Microbial Metabolism of Polyphenols. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2016; 15:425-444. [PMID: 27274718 PMCID: PMC4888912 DOI: 10.1007/s11101-016-9459-z] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 03/02/2016] [Indexed: 05/18/2023]
Abstract
Gut microbiota contribute to the metabolism of dietary polyphenols and affect the bioavailability of both the parent polyphenols and their metabolites. Although there is a large number of reports of specific polyphenol metabolites, relatively little is known regarding the chemistry and enzymology of the metabolic pathways utilized by specific microbial species and taxa, which is the focus of this review. Major classes of dietary polyphenols include monomeric and oligomeric catechins (proanthocyanidins), flavonols, flavanones, ellagitannins, and isoflavones. Gut microbial metabolism of representatives of these polyphenol classes can be classified as A- and C-ring cleavage (retro Claisen reactions), C-ring cleavage mediated by dioxygenases, dehydroxylations (decarboxylation or reduction reactions followed by release of H2O molecules), and hydrogenations of alkene moieties in polyphenols, such as resveratrol, curcumin, and isoflavones (mediated by NADPH-dependent reductases). The qualitative and quantitative metabolic output of the gut microbiota depends to a large extent on the metabolic capacity of individual taxa, which emphasizes the need for assessment of functional analysis in conjunction with determinations of gut microbiota compositions.
Collapse
Affiliation(s)
- Jan F Stevens
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97330; Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97330
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97330; Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97330
| |
Collapse
|
20
|
Sun YJ, Huang QQ, Li P, Zhang JJ. Catalytic dioxygenation of flavonol by M(II)-complexes (M = Mn, Fe, Co, Ni, Cu and Zn) - mimicking the M(II)-substituted quercetin 2,3-dioxygenase. Dalton Trans 2016; 44:13926-38. [PMID: 26153684 DOI: 10.1039/c5dt01760b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In order to get insights into the metal ion effects and the carboxylate effects on enzymatic activity, a series of the carboxylate ligand supported transition metal complexes [M(II)L(OAc)] (M = Mn (), Fe (), Co (), Ni (), Cu () and Zn (); LH = 2-{[bis-(pyridin-2-ylmethyl)amino]methyl}-4-methoxy benzoic acid) were synthesized and characterized as structural and functional models for the active sites of various M(II)-substituted resting quercetin 2,3-dioxygenases (2,3-QD). Their structures, spectroscopic features, redox properties, as well as the catalytic reactivity toward the substrate flavonol and O2 have been investigated in detail. The model complexes show higher enzymatic reactivities in the catalytic dioxygenation (oxidative ring opening) of the substrate flavonol at lower temperatures (55-100 °C), presumably caused by the carboxylate group in the supporting model ligand, which could lower the redox potential of the bound substrate flavonolate by electron donation. The catalytic reactivity of [M(II)L(OAc)] exhibits notable differences and it is in a metal ion dependent order of Co () > Ni () > Zn () > Fe () > Mn () > Cu (). The differences in the reactivities among them could be ascribed to the redox potential of the bound substrate flavonolate, which was drastically influenced by the metal ions via tuning the electron density of flavonolate, providing important insights into the metal ion effects and the carboxylate effects on the enzymatic activity of various M(II)-substituted 2,3-QD. Our model complexes [M(II)L(OAc)] are the first examples of a series of structural and functional models of various M(II)-substituted resting 2,3-QD.
Collapse
Affiliation(s)
- Ying-Ji Sun
- Department of Chemistry, Dalian University of Technology, Linggong Road 2, 116024, Dalian, China.
| | | | | | | |
Collapse
|
21
|
Wojdyła Z, Borowski T. DFT study of the mechanism of manganese quercetin 2,3-dioxygenase: quest for origins of enzyme unique nitroxygenase activity and regioselectivity. J Biol Inorg Chem 2016; 21:475-89. [DOI: 10.1007/s00775-016-1356-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
|
22
|
Fang Z, Dos Santos PC. Protective role of bacillithiol in superoxide stress and Fe-S metabolism in Bacillus subtilis. Microbiologyopen 2015; 4:616-31. [PMID: 25988368 PMCID: PMC4554457 DOI: 10.1002/mbo3.267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 01/22/2023] Open
Abstract
Glutathione (GSH) serves as the prime thiol in most organisms as its depletion increases antibiotic and metal toxicity, impairs oxidative stress responses, and affects Fe and Fe–S cluster metabolism. Many gram-positive bacteria lack GSH, but instead produce other structurally unrelated yet functionally equivalent thiols. Among those, bacillithiol (BSH) has been recently identified in several low G+C gram-positive bacteria. In this work, we have explored the link between BSH and Fe–S metabolism in Bacillus subtilis. We have identified that B. subtilis lacking BSH is more sensitive to oxidative stress (paraquat), and metal toxicity (Cu(I) and Cd(II)), but not H2O2. Furthermore, a slow growth phenotype of BSH null strain in minimal medium was observed, which could be recovered upon the addition of selected amino acids (Leu/Ile and Glu/Gln), supplementation of iron, or chemical complementation with BSH disulfide (BSSB) to the growth medium. Interestingly, Fe–S cluster containing isopropylmalate isomerase (LeuCD) and glutamate synthase (GOGAT) showed decreased activities in BSH null strain. Deficiency of BSH also resulted in decreased levels of intracellular Fe accompanied by increased levels of manganese and altered expression levels of Fe–S cluster biosynthetic SUF components. Together, this study is the first to establish a link between BSH and Fe–S metabolism in B. subtilis.
Collapse
Affiliation(s)
- Zhong Fang
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, 27016
| | - Patricia C Dos Santos
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, 27016
| |
Collapse
|
23
|
Nianios D, Thierbach S, Steimer L, Lulchev P, Klostermeier D, Fetzner S. Nickel quercetinase, a "promiscuous" metalloenzyme: metal incorporation and metal ligand substitution studies. BMC BIOCHEMISTRY 2015; 16:10. [PMID: 25903361 PMCID: PMC4416304 DOI: 10.1186/s12858-015-0039-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/01/2015] [Indexed: 11/12/2022]
Abstract
BACKGROUND Quercetinases are metal-dependent dioxygenases of the cupin superfamily. While fungal quercetinases are copper proteins, recombinant Streptomyces quercetinase (QueD) was previously described to be capable of incorporating Ni(2+) and some other divalent metal ions. This raises the questions of which factors determine metal selection, and which metal ion is physiologically relevant. RESULTS Metal occupancies of heterologously produced QueD proteins followed the order Ni > Co > Fe > Mn. Iron, in contrast to the other metals, does not support catalytic activity. QueD isolated from the wild-type Streptomyces sp. strain FLA contained mainly nickel and zinc. In vitro synthesis of QueD in a cell-free transcription-translation system yielded catalytically active protein when Ni(2+) was present, and comparison of the circular dichroism spectra of in vitro produced proteins suggested that Ni(2+) ions support correct folding. Replacement of individual amino acids of the 3His/1Glu metal binding motif by alanine drastically reduced or abolished quercetinase activity and affected its structural integrity. Only substitution of the glutamate ligand (E76) by histidine resulted in Ni- and Co-QueD variants that retained the native fold and showed residual catalytic activity. CONCLUSIONS Heterologous formation of catalytically active, native QueD holoenzyme requires Ni(2+), Co(2+) or Mn(2+), i.e., metal ions that prefer an octahedral coordination geometry, and an intact 3His/1Glu motif or a 4His environment of the metal. The observed metal occupancies suggest that metal incorporation into QueD is governed by the relative stability of the resulting metal complexes, rather than by metal abundance. Ni(2+) most likely is the physiologically relevant cofactor of QueD of Streptomyces sp. FLA.
Collapse
Affiliation(s)
- Dimitrios Nianios
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, Corrensstrasse 3, Muenster, D-48149, Germany.
| | - Sven Thierbach
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, Corrensstrasse 3, Muenster, D-48149, Germany.
| | - Lenz Steimer
- Institute of Physical Chemistry, University of Muenster, Corrensstrasse 30, Muenster, D-48149, Germany.
| | - Pavel Lulchev
- Institute of Physical Chemistry, University of Muenster, Corrensstrasse 30, Muenster, D-48149, Germany.
| | - Dagmar Klostermeier
- Institute of Physical Chemistry, University of Muenster, Corrensstrasse 30, Muenster, D-48149, Germany.
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, Corrensstrasse 3, Muenster, D-48149, Germany.
| |
Collapse
|
24
|
Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1112] [Impact Index Per Article: 111.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| |
Collapse
|
25
|
Sun YJ, Huang QQ, Zhang JJ. Series of Structural and Functional Models for the ES (Enzyme–Substrate) Complex of the Co(II)-Containing Quercetin 2,3-Dioxygenase. Inorg Chem 2014; 53:2932-42. [DOI: 10.1021/ic402695c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ying-Ji Sun
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Qian-Qian Huang
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Jian-Jun Zhang
- School of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| |
Collapse
|
26
|
Sun YJ, Huang QQ, Zhang JJ. A series of NiII-flavonolate complexes as structural and functional ES (enzyme-substrate) models of the NiII-containing quercetin 2,3-dioxygenase. Dalton Trans 2014; 43:6480-9. [DOI: 10.1039/c3dt53349b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
27
|
|
28
|
Matuz A, Giorgi M, Speier G, Kaizer J. Structural and functional comparison of manganese-, iron-, cobalt-, nickel-, and copper-containing biomimic quercetinase models. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
29
|
Sun YJ, Huang QQ, Tano T, Itoh S. Flavonolate Complexes of MII (M = Mn, Fe, Co, Ni, Cu, and Zn). Structural and Functional Models for the ES (Enzyme–Substrate) Complex of Quercetin 2,3-Dioxygenase. Inorg Chem 2013; 52:10936-48. [DOI: 10.1021/ic400972k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ying-Ji Sun
- School
of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Qian-Qian Huang
- School
of Chemistry, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Tetsuro Tano
- Department
of Material and Life Science, Division of Advanced Science and Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shinobu Itoh
- Department
of Material and Life Science, Division of Advanced Science and Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
30
|
Uberto R, Moomaw EW. Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PLoS One 2013; 8:e74477. [PMID: 24040257 PMCID: PMC3765361 DOI: 10.1371/journal.pone.0074477] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/01/2013] [Indexed: 12/11/2022] Open
Abstract
The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional clustering. Networks based only on cupin domains and networks based on the whole proteins provide complementary information. Domain-clustering supports phylogenetic conclusions that the N- and C-terminal domains of bicupin proteins evolved independently. Interestingly, although many functionally similar enzymatic cupin members bind the same active site metal ion, the structure and sequence clustering does not correlate with the identity of the bound metal. It is anticipated that the application of PSNs to this superfamily will inform experimental work and influence the functional annotation of databases.
Collapse
Affiliation(s)
- Richard Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ellen W. Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
| |
Collapse
|
31
|
Buongiorno D, Straganz GD. Structure and function of atypically coordinated enzymatic mononuclear non-heme-Fe(II) centers. Coord Chem Rev 2013; 257:541-563. [PMID: 24850951 PMCID: PMC4019311 DOI: 10.1016/j.ccr.2012.04.028] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 11/17/2022]
Abstract
Mononuclear, non-heme-Fe(II) centers are key structures in O2 metabolism and catalyze an impressive variety of enzymatic reactions. While most are bound via two histidines and a carboxylate, some show a different organization. A short overview of atypically coordinated O2 dependent mononuclear-non-heme-Fe(II) centers is presented here Enzymes with 2-His, 3-His, 3-His-carboxylate and 4-His bound Fe(II) centers are discussed with a focus on their reactivity, metal ion promiscuity and recent progress in the elucidation of their enzymatic mechanisms. Observations concerning these and classically coordinated Fe(II) centers are used to understand the impact of the metal binding motif on catalysis.
Collapse
Key Words
- 1,3-bis(2-pyridylimino)isoindoline, ind
- 2OH-1,3-Ph2PD, 2-hydroxy-1,3-diphenylpropanedione
- 6-Ph2TPA, N,N-bis[(6-phenyl-2-pyridyl)methyl]-N-[(2-pyridyl)-methyl]amine
- ADO, cysteamine dioxygenase
- AO, apocarotenoid 15,15′-oxygenase
- ARD, aci-reductone dioxygenase
- BsQDO, quercetin 2,3-dioxygenase from Bacillus subtilis
- CD, circular dichroism
- CDO, cysteine dioxygenase
- CGDO, 5-chloro-gentisate 1,2-dioxygenase
- CS2, clavaminate synthase
- CarOs, carotenoid oxygenases
- DFT, density functional theory
- Dioxygen activation
- Dioxygenase
- Dke1, diketone dioxygenase
- EPR, electron paramagnetic resonance
- EXAFS, extended X-ray absorption fine structure spectroscopy
- Enzyme catalysis
- Facial triad
- GDO, gentisate 1,2-dioxygenase
- HADO, 3-hydroxyanthranilate 3,4-dioxygenase
- HGDO, homogentisate 1,2-dioxygenase
- HNDO, hydroxy-2-naphthoate dioxygenase
- MCD, magnetic circular dichroism
- MNHEs, mononuclear non-heme-Fe(II) dependent enzymes
- Metal binding motif
- NRP, nonribosomal peptide
- OTf-, trifluormethanesulfonate
- PDB, protein data bank
- QDO, quercetin 2,3-dioxygenase
- SDO, salicylate 1,2-dioxygenase
- Structure–function relationships
- TauD, taurine hydroxylase
- XAS, X-ray absorption spectroscopy
- acac, acetylacetone (2,4-pentanedione)
- fla, flavonolate
- α-KG, α-ketoglutarate
Collapse
Affiliation(s)
- Daniela Buongiorno
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12 A-8010 Graz, Austria
| | - Grit D Straganz
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12 A-8010 Graz, Austria
| |
Collapse
|
32
|
Marin AM, Souza EM, Pedrosa FO, Souza LM, Sassaki GL, Baura VA, Yates MG, Wassem R, Monteiro RA. Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1. MICROBIOLOGY-SGM 2012; 159:167-175. [PMID: 23125118 DOI: 10.1099/mic.0.061135-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several bacteria are able to degrade flavonoids either to use them as carbon sources or as a detoxification mechanism. Degradation pathways have been proposed for several bacteria, but the genes responsible are not known. We identified in the genome of the endophyte Herbaspirillum seropedicae SmR1 an operon potentially associated with the degradation of aromatic compounds. We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids. Mutation of fdeA, the first gene of the operon, and fdeR, its transcriptional activator, abolished the ability of H. seropedicae to degrade naringenin.
Collapse
Affiliation(s)
- A M Marin
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - E M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - F O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - L M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - G L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - V A Baura
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - M G Yates
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - R Wassem
- Department of Genetics, Universidade Federal do Paraná, CP 19071, 81531-980, Curitiba, PR, Brazil
| | - R A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| |
Collapse
|
33
|
Oxygenolysis reaction mechanism of copper-dependent quercetin 2,3-dioxygenase: A density functional theory study. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4729-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
34
|
Bio-inspired flavonol and quinolone dioxygenation by a non-heme iron catalyst modeling the action of flavonol and 3-hydroxy-4(1H)-quinolone 2,4-dioxygenases. J Inorg Biochem 2012; 108:15-21. [DOI: 10.1016/j.jinorgbio.2011.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/27/2011] [Accepted: 11/15/2011] [Indexed: 11/24/2022]
|
35
|
Abstract
Ring-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject to ortho or meta cleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an Fe(II) center for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O(2), resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O(2) is supported by model chemistry.
Collapse
|
36
|
Nitrosyl hydride (HNO) replaces dioxygen in nitroxygenase activity of manganese quercetin dioxygenase. Proc Natl Acad Sci U S A 2011; 108:18926-31. [PMID: 22084064 DOI: 10.1073/pnas.1111488108] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quercetin dioxygenase (QDO) catalyzes the oxidation of the flavonol quercetin with dioxygen, cleaving the central heterocyclic ring and releasing CO. The QDO from Bacillus subtilis is unusual in that it has been shown to be active with several divalent metal cofactors such as Fe, Mn, and Co. Previous comparison of the catalytic activities suggest that Mn(II) is the preferred cofactor for this enzyme. We herein report the unprecedented substitution of nitrosyl hydride (HNO) for dioxygen in the activity of Mn-QDO, resulting in the incorporation of both N and O atoms into the product. Turnover is demonstrated by consumption of quercetin and other related substrates under anaerobic conditions in the presence of HNO-releasing compounds and the enzyme. As with dioxygenase activity, a nonenzymatic base-catalyzed reaction of quercetin with HNO is observed above pH 7, but no enhancement of this basal reactivity is found upon addition of divalent metal salts. Unique and regioselective N-containing products ((14)N/(15)N) have been characterized by MS analysis for both the enzymatic and nonenzymatic reactions. Of the several metallo-QDO enzymes examined for nitroxygenase activity under anaerobic condition, only the Mn(II) is active; the Fe(II) and Co(II) substituted enzymes show little or no activity. This result represents an enzymatic catalysis which we denote nitroxygenase activity; the unique reactivity of the Mn-QDO suggests a metal-mediated electron transfer mechanism rather than metal activation of the substrate's inherent base-catalyzed reactivity.
Collapse
|
37
|
Identification of aromatic residues critical to the DNA binding and ligand response of the Bacillus subtilis QdoR (YxaF) repressor antagonized by flavonoids. Biosci Biotechnol Biochem 2011; 75:1325-34. [PMID: 21737930 DOI: 10.1271/bbb.110098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bacillus subtilis LmrA and QdoR (formerly YxaF) are paralogous transcriptional regulators that repress their regulon comprising the lmrAB operon, the qdoR gene, and the qdoI-yxaH operon, by binding to the LmrA/QdoR boxes located in the promoter regions. Detachment of them followed by derepression of the target genes is induced by certain flavonoids. To identify the residues critical to the ligand response in QdoR, we selected eight residues based on structural information, produced eight single-mutated QdoRs in which each residue was replaced with alanine, and evaluated their capacities for DNA binding and the flavonoid response by gel retardation analysis. The three mutants, carrying the alanine substitution at Phe87, Trp131, or Phe135, showed features distinctly different from those of the wild type and from each other. We further examined the in vivo function of the mutant with alanine substitution at Trp131 by reporter assay. This largely supported the corresponding in vitro results. The in vitro and in vivo data suggest that Phe87, Trp131, and Phe135, forming a hydrophobic cluster in QdoR, play crucial roles in the DNA binding, flavonoid accommodation, and/or conformational change triggered by ligand binding.
Collapse
|
38
|
Moussatche P, Angerhofer A, Imaram W, Hoffer E, Uberto K, Brooks C, Bruce C, Sledge D, Richards NGJ, Moomaw EW. Characterization of Ceriporiopsis subvermispora bicupin oxalate oxidase expressed in Pichia pastoris. Arch Biochem Biophys 2011; 509:100-7. [PMID: 21376010 PMCID: PMC3078958 DOI: 10.1016/j.abb.2011.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/23/2011] [Accepted: 02/24/2011] [Indexed: 01/16/2023]
Abstract
Oxalate oxidase (E.C. 1.2.3.4) catalyzes the oxygen-dependent oxidation of oxalate to carbon dioxide in a reaction that is coupled with the formation of hydrogen peroxide. Although there is currently no structural information available for oxalate oxidase from Ceriporiopsis subvermispora (CsOxOx), sequence data and homology modeling indicate that it is the first manganese-containing bicupin enzyme identified that catalyzes this reaction. Interestingly, CsOxOx shares greatest sequence homology with bicupin microbial oxalate decarboxylases (OxDC). We show that CsOxOx activity directly correlates with Mn content and other metals do not appear to be able to support catalysis. EPR spectra indicate that the Mn is present as Mn(II), and are consistent with the coordination environment expected from homology modeling with known X-ray crystal structures of OxDC from Bacillus subtilis. EPR spin-trapping experiments support the existence of an oxalate-derived radical species formed during turnover. Acetate and a number of other small molecule carboxylic acids are competitive inhibitors for oxalate in the CsOxOx catalyzed reaction. The pH dependence of this reaction suggests that the dominant contribution to catalysis comes from the monoprotonated form of oxalate binding to a form of the enzyme in which an active site carboxylic acid residue must be unprotonated.
Collapse
Affiliation(s)
- Patricia Moussatche
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Alexander Angerhofer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Witcha Imaram
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Eric Hoffer
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| | - Kelsey Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| | - Christopher Brooks
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Crystal Bruce
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Daniel Sledge
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Ellen W. Moomaw
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| |
Collapse
|
39
|
The rutin catabolic pathway with special emphasis on quercetinase. Biodegradation 2010; 21:833-59. [DOI: 10.1007/s10532-010-9359-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Accepted: 04/08/2010] [Indexed: 10/19/2022]
|
40
|
Grubel K, Rudzka K, Arif AM, Klotz KL, Halfen JA, Berreau LM. Synthesis, Characterization, and Ligand Exchange Reactivity of a Series of First Row Divalent Metal 3-Hydroxyflavonolate Complexes. Inorg Chem 2009; 49:82-96. [DOI: 10.1021/ic901405h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Katarzyna Grubel
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Katarzyna Rudzka
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Atta M. Arif
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
| | - Katie L. Klotz
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702
| | - Jason A. Halfen
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702
| | - Lisa M. Berreau
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
| |
Collapse
|
41
|
Moomaw EW, Angerhofer A, Moussatche P, Ozarowski A, García-Rubio I, Richards NGJ. Metal dependence of oxalate decarboxylase activity. Biochemistry 2009; 48:6116-25. [PMID: 19473032 PMCID: PMC2801813 DOI: 10.1021/bi801856k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis oxalate decarboxylase (OxDC) catalyzes the conversion of oxalate into CO(2) and formate. The enzyme is composed of two cupin domains, each of which contains a Mn(II) ion. Although there is general agreement that Mn(II) in the N-terminal domain mediates OxDC-catalyzed decarboxylation, legitimate questions have been raised concerning the function (if any) of the Mn(II) bound in the C-terminal cupin domain. We have investigated this problem using a series of OxDC mutants in which Mn(II) binding is perturbed by mutagenesis of Glu-101 and Glu-280, which coordinate the metal in the N-terminal and C-terminal domains, respectively. We now demonstrate that decarboxylase activity and total manganese content are sensitive to modifications in either metal-binding glutamate residue. These findings, in combination with EPR measurements, raise the possibility that the C-terminal Mn(II) center can catalyze the decarboxylation reaction. Further support for this conclusion has been provided from a combination of in vivo and in vitro strategies for preparing wild-type OxDC in which Mn(II) is incorporated to a variety of extents. Kinetic characterization of these variants shows that OxDC activity is linearly correlated with manganese content, as might be expected if both sites can catalyze the breakdown of oxalate into formate and CO(2). These studies also represent the first unequivocal demonstration that OxDC activity is uniquely mediated by manganese.
Collapse
Affiliation(s)
- Ellen W. Moomaw
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | | | - Patricia Moussatche
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-3706
| | - Inés García-Rubio
- Laboratorium fur Physikalische Chemie, ETH Zurich, CH-8043 Zurich-Hönggerberg, Switzerland
| | | |
Collapse
|
42
|
Regulation of the Bacillus subtilis divergent yetL and yetM genes by a transcriptional repressor, YetL, in response to flavonoids. J Bacteriol 2009; 191:3685-97. [PMID: 19329649 DOI: 10.1128/jb.00202-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA microarray analysis revealed that transcription of the Bacillus subtilis yetM gene encoding a putative flavin adenine dinucleotide-dependent monooxygenase was triggered by certain flavonoids during culture and was derepressed by disruption of the yetL gene in the opposite orientation situated immediately upstream of yetM, which encodes a putative MarR family transcriptional regulator. In vitro analyses, including DNase I footprinting and gel retardation analysis, indicated that YetL binds specifically to corresponding single sites in the divergent yetL and yetM promoter regions, with higher affinity to the yetM region; the former region overlaps the Shine-Dalgarno sequence of yetL, and the latter region contains a perfect 18-bp palindromic sequence (TAGTTAGGCGCCTAACTA). In vitro gel retardation and in vivo lacZ fusion analyses indicated that some flavonoids (kaempferol, apigenin, and luteolin) effectively inhibit YetL binding to the yetM cis sequence, but quercetin, galangin, and chrysin do not inhibit this binding, implying that the 4-hydroxyl group on the B-ring of the flavone structure is indispensable for this inhibition and that the coexistence of the 3-hydroxyl groups on the B- and C-rings does not allow antagonism of YetL.
Collapse
|
43
|
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol 2009; 388:356-80. [PMID: 19265704 DOI: 10.1016/j.jmb.2009.02.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 11/24/2022]
Abstract
In metalloproteins, the protein environment modulates metal properties to achieve the required goal, which can be protein stabilization or function. The analysis of metal sites at the atomic level of detail provided by protein structures can thus be of benefit in functional and evolutionary studies of proteins. In this work, we propose a structural bioinformatics approach to the study of metalloproteins based on structural templates of metal sites that include the PDB coordinates of protein residues forming the first and the second coordination sphere of the metal. We have applied this approach to non-heme iron sites, which have been analyzed at various levels. Templates of sites located in different protein domains have been compared, showing that similar sites can be found in unrelated proteins as the result of convergent evolution. Templates of sites located in proteins of a large superfamily have been compared, showing possible mechanisms of divergent evolution of proteins to achieve different functions. Furthermore, template comparisons have been used to predict the function of uncharacterized proteins, showing that similarity searches focused on metal sites can be advantageously combined with typical whole-domain comparisons. Structural templates of metal sites, finally, may constitute the basis for a systematic classification of metalloproteins in databases.
Collapse
Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | | | | | | | | |
Collapse
|
44
|
Baráth G, Kaizer J, Speier G, Párkányi L, Kuzmann E, Vértes A. One metal–two pathways to the carboxylate-enhanced, iron-containing quercetinase mimics. Chem Commun (Camb) 2009:3630-2. [DOI: 10.1039/b903224j] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
45
|
Merkens H, Kappl R, Jakob RP, Schmid FX, Fetzner S. Quercetinase QueD of Streptomyces sp. FLA, a Monocupin Dioxygenase with a Preference for Nickel and Cobalt. Biochemistry 2008; 47:12185-96. [DOI: 10.1021/bi801398x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hedda Merkens
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany, Fachrichtung 2.5 Biophysik, Universität des Saarlandes, Klinikum Geb. 76, 66421 Homburg/Saar, Germany, and Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Reinhard Kappl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany, Fachrichtung 2.5 Biophysik, Universität des Saarlandes, Klinikum Geb. 76, 66421 Homburg/Saar, Germany, and Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Roman P. Jakob
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany, Fachrichtung 2.5 Biophysik, Universität des Saarlandes, Klinikum Geb. 76, 66421 Homburg/Saar, Germany, and Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X. Schmid
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany, Fachrichtung 2.5 Biophysik, Universität des Saarlandes, Klinikum Geb. 76, 66421 Homburg/Saar, Germany, and Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Susanne Fetzner
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany, Fachrichtung 2.5 Biophysik, Universität des Saarlandes, Klinikum Geb. 76, 66421 Homburg/Saar, Germany, and Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
46
|
Malkhasian AYS, Finch ME, Pawlak PL, Anderson JM, Brennessel WW, Chavez FA. Synthesis, Structure, and Characterization of Dichloro-(1-Benzyl-4-Acetato-1,4,7-Triazacyclononane)Iron(III). Z Anorg Allg Chem 2008. [DOI: 10.1002/zaac.200800014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
47
|
Tranchimand S, Ertel G, Gaydou V, Gaudin C, Tron T, Iacazio G. Biochemical and molecular characterization of a quercetinase from Penicillium olsonii. Biochimie 2007; 90:781-9. [PMID: 18206655 DOI: 10.1016/j.biochi.2007.12.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 12/14/2007] [Indexed: 11/19/2022]
Abstract
Quercetinase (quercetin 2,3-dioxygenase, EC 1.13.11.24) is produced by various filamentous fungi when grown on rutin as the sole carbon and energy source. From a rutin based liquid culture of Penicillium olsonii, we purified a quercetinase with a specific activity of 175U mg(-1). The enzyme is a monomeric glycoprotein of approximately 55 kDa, containing 0.9+/-0.1 copper atoms per protein. Its substrate specificity is restricted to the flavonol family of flavonoids. It is completely inhibited by diethyldithiocarbamate at a concentration of 100 nM and 1H-2-benzyl-3-hydroxy-4-oxoquinolin is a competitive inhibitor with a K(I) of 4 microM. The cDNA poquer1 was cloned and sequenced. It encodes a 365 amino acids long enzyme with a strong sequence identity with the Aspergillus japonicus quercetinase (Q7SIC2). Like the enzyme from A. japonicus, only one of the two cupin domains of the Penicillium olsonii quercetinase is able to bind a metal atom.
Collapse
Affiliation(s)
- Sylvain Tranchimand
- Laboratoire BiosCiences FRE CNRS 3005, case 432, Faculté des Sciences et Techniques de Saint Jérôme, Aix-Marseille Université, avenue Escadrille Normandie-Niemen, 133397 Marseille Cedex 20, France
| | | | | | | | | | | |
Collapse
|
48
|
Straganz GD, Nidetzky B. Variations of the 2-His-1-carboxylate theme in mononuclear non-heme FeII oxygenases. Chembiochem 2007; 7:1536-48. [PMID: 16858718 DOI: 10.1002/cbic.200600152] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A facial triad of two histidine side chains and one aspartate or glutamate side chain forms the canonical metal-coordinating motif in the catalytic centers of various mononuclear non-heme Fe(II) enzymes. Although these active sites are based on totally unrelated protein folds and bring about a wide range of chemical transformations, most of them share the ability to couple dioxygen reduction with the oxygenation of an organic substrate. With the increasing number of protein structures now solved, it has become clear that the 2-His-1-carboxylate signature is less of a paradigm for non-heme Fe(II) active sites than had long been thought and that it can be replaced by alternative metal centers in various oxygenases, the structure-function relationships and proposed catalytic mechanisms of which are reviewed here. Metal coordination through three histidines and one glutamate constitutes the classical motif described for enzyme members of the cupin protein superfamily, such as aci-reductone dioxygenase and quercetin dioxygenase, multiple metal forms of which (including the Fe(II) type) are found in nature. Cysteine dioxygenase and diketone dioxygenase, which are strictly Fe(II)-dependent oxygenases based on the cupin fold, bind the catalytic metal through the homologous triad of histidines, but lack the fourth glutamate ligand. An alpha-ketoglutarate-dependent Fe(II) halogenase shows metal coordination by two histidines as the only protein-derived ligands, whilst carotene oxygenase, from a different protein fold family, features an Fe(II) site consisting of four histidine side chains. These recently discovered metallocenters are discussed with respect to their metal-binding properties and the reaction coordinates of the O(2)-dependent conversions they catalyze.
Collapse
Affiliation(s)
- G D Straganz
- Institute of Biotechnology and Biochemical Engineering Graz University of Technology Petersgasse 12/I, 8010 Graz, Austria.
| | | |
Collapse
|
49
|
Hirooka K, Kunikane S, Matsuoka H, Yoshida KI, Kumamoto K, Tojo S, Fujita Y. Dual regulation of the Bacillus subtilis regulon comprising the lmrAB and yxaGH operons and yxaF gene by two transcriptional repressors, LmrA and YxaF, in response to flavonoids. J Bacteriol 2007; 189:5170-82. [PMID: 17483215 PMCID: PMC1951842 DOI: 10.1128/jb.00079-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis LmrA is known to be a repressor that regulates the lmrAB and yxaGH operons; lmrB and yxaG encode a multidrug resistance pump and quercetin 2,3-dioxygenase, respectively. DNase I footprinting analysis revealed that LmrA and YxaF, which are paralogous to each other, bind specifically to almost the same cis sequences, LmrA/YxaF boxes, located in the promoter regions of the lmrAB operon, the yxaF gene, and the yxaGH operon for their repression and containing a consensus sequence of AWTATAtagaNYGgTCTA, where W, Y, and N stand for A or T, C or T, and any base, respectively (three-out-of-four match [in lowercase type]). Gel retardation analysis indicated that out of the eight flavonoids tested, quercetin, fisetin, and catechin are most inhibitory for LmrA to DNA binding, whereas quercetin, fisetin, tamarixetin, and galangin are most inhibitory for YxaF. Also, YxaF bound most tightly to the tandem LmrA/YxaF boxes in the yxaGH promoter region. The lacZ fusion experiments essentially supported the above-mentioned in vitro results, except that galangin did not activate the lmrAB and yxaGH promoters, probably due to its poor incorporation into cells. Thus, the LmrA/YxaF regulon presumably comprising the lmrAB operon, the yxaF gene, and the yxaGH operon is induced in response to certain flavonoids. The in vivo experiments to examine the regulation of the synthesis of the reporter beta-galactosidase and quercetin 2,3-dioxgenase as well as that of multidrug resistance suggested that LmrA represses the lmrAB and yxaGH operons but that YxaF represses yxaGH more preferentially.
Collapse
Affiliation(s)
- Kazutake Hirooka
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, 985 Sanzo, Higashimura, Fukuyama 729-0292, Japan
| | | | | | | | | | | | | |
Collapse
|
50
|
Merkens H, Sielker S, Rose K, Fetzner S. A new monocupin quercetinase of Streptomyces sp. FLA: identification and heterologous expression of the queD gene and activity of the recombinant enzyme towards different flavonols. Arch Microbiol 2007; 187:475-87. [PMID: 17516049 DOI: 10.1007/s00203-007-0215-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2006] [Revised: 11/18/2006] [Accepted: 01/11/2007] [Indexed: 10/23/2022]
Abstract
The gene queD encoding quercetinase of Streptomyces sp. FLA, a soil isolate related to S. eurythermus (T), was identified. Quercetinases catalyze the 2,4-dioxygenolytic cleavage of 3,5,7,3',4'-pentahydroxyflavone to 2-protocatechuoylphloroglucinol carboxylic acid and carbon monoxide. The queD gene was expressed in S. lividans and E. coli, and the recombinant hexahistidine-tagged protein (QueDHis(6)) was purified. Several flavonols were converted by QueDHis(6), whereas CO formation from the 2,3-dihydroflavonol taxifolin and the flavone luteolin were not observed. In contrast to bicupin quercetinases from Aspergillus japonicus and Bacillus subtilis, and bicupin pirins showing quercetinase activity, QueD of strain FLA is a monocupin exhibiting 35.9% sequence identity to the C-terminal domain of B. subtilis quercetinase. Its native molecular mass of 63 kDa suggests a multimeric protein. A queD-specific probe hybridized with fragments of genomic DNA of four other quercetin degrading Streptomyces strains, but not with DNA of B. subtilis. Potential ORFs upstream of queD probably code for a serine protease and an endoribonuclease; two ORFs downstream of queD may encode an amidohydrolase and a carboxylesterase. This arrangement suggests that queD is not part of a catabolic gene cluster. Quercetinases might play a major role as detoxifying rather than catabolic enzymes.
Collapse
Affiliation(s)
- Hedda Merkens
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstr. 3, 48149 Münster, Germany
| | | | | | | |
Collapse
|