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Li Y, Xu T, Tu Y, Li T, Wei Y, Zhou Y. An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085. Appl Environ Microbiol 2024; 90:e0104724. [PMID: 39028195 PMCID: PMC11337842 DOI: 10.1128/aem.01047-24] [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: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is a key intermediate in the degradation of polyphenols such as flavonoids and hydrolysable tannins and can be used by certain bacteria as a carbon and energy source for growth. The identification of enzymes that participate in the fermentation of phloroglucinol to acetate and butyrate in Clostridia was recently reported. In this study, we present the discovery and characterization of a novel metabolic pathway for phloroglucinol degradation in the bacterium Collinsella sp. zg1085, from marmot respiratory tract. In both the Clostridial and Collinsella pathways, phloroglucinol is first reduced to dihydrophoroglucinol by the NADPH-dependent phloroglucinol reductase (PGR), followed by ring opening to form (S)-3-hydroxy-5-oxohexanoate by a Mn2+-dependent dihydrophloroglucinol cyclohydrolase (DPGC). In the Collinsella pathway, (S)-3-hydroxy-5-oxohexanoate is then cleaved to form malonate semialdehyde and acetone by a newly identified aldolase (HOHA). Finally, a NADP+-dependent malonate-semialdehyde dehydrogenase converts malonate semialdehyde to CO2 and acetyl-CoA, an intermediate in carbon and energy metabolism. Recombinant expression of the Collinsella PGR, DPGC, and HOHA in E. coli enabled the conversion of phloroglucinol into acetone, providing support for the proposed pathway. Experiments with Olsenella profusa, another bacterium containing the gene cluster of interest, show that the PGR, DPGC, HOHA, and MSDH are induced by phloroglucinol. Our findings add to the variety of metabolic pathways for the degradation of phloroglucinol, a widely distributed phenolic compound, in the anaerobic microbiome.IMPORTANCEPhloroglucinol is an important intermediate in the bacterial degradation of polyphenols, a highly abundant class of plant natural products. Recent research has identified key enzymes of the phloroglucinol degradation pathway in butyrate-producing anaerobic bacteria, which involves cleavage of a linear triketide intermediate by a beta ketoacid cleavage enzyme, requiring acetyl-CoA as a co-substrate. This paper reports a variant of the pathway in the lactic acid bacterium Collinsella sp. zg1085, which involves cleavage of the triketide intermediate by a homolog of deoxyribose-5-phosphate aldolase, highlighting the variety of mechanisms for phloroglucinol degradation by different anaerobic bacterial taxa.
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Affiliation(s)
- Yating Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Xu
- Department of Pharmacy, Northern Jiangsu People’s Hospital, Clinical Medical School of Yangzhou University, Yangzhou, Jiangsu, China
| | - Yanqin Tu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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Maigaard M, Weisbjerg MR, Hellwing ALF, Larsen M, Andersen FB, Lund P. The acute effects of rumen pulse-dosing of hydrogen acceptors during methane inhibition with nitrate or 3-nitrooxypropanol in dairy cows. J Dairy Sci 2024; 107:5681-5698. [PMID: 38608947 DOI: 10.3168/jds.2023-24343] [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: 10/24/2023] [Accepted: 03/03/2024] [Indexed: 04/14/2024]
Abstract
Dietary methane (CH4) mitigation is in some cases associated with an increased hydrogen (H2) emission. The objective of the present study was to investigate the acute and short-term effects of acceptors for H2 (fumaric acid, acrylic acid, or phloroglucinol) supplemented via pulse-dosing to dairy cows fed CH4 mitigating diets (using nitrate or 3-nitrooxypropanol), on gas exchange, rumen gas, and VFA composition. For this purpose, 2 individual 4 × 4 Latin square experiments were conducted with 4 periods of 3 d (nitrate supplementation) and 7 d (3-nitrooxypropanol supplementation), respectively. In each study, 4 rumen-cannulated Danish Holstein cows were used. Each additive for CH4 mitigation was included in the ad libitum-fed diet within the 2 experiments (exp. 1 and exp. 2), to which the cows were adapted for at least 14 d. Acceptors for H2 were administered twice daily in equal portions through the rumen fistula immediately after feeding of the individual cow. In exp. 1 (nitrate), the treatments were CON-1 (no H2-acceptor), FUM-1 (fumaric acid), ACR-1 (acrylic acid), and FUM+ACR-1 (50% FUM-1 + 50% ACR-1). In exp. 2 (3-nitrooxypropanol), the 3 treatments, CON-2, FUM-2, and ACR-2, were similar to CON-1, FUM-1 and ACR-1 treatments, however the fourth treatment was PHL-2 (phloroglucinol). Gas exchanges were measured in respiration chambers, and samples of rumen liquid and headspace gas were taken in time series relative to feeding and dosing on specific days. Headspace gas was analyzed for gas composition, and rumen liquid was analyzed for VFA composition and dissolved gas concentrations. Headspace gas composition and dissolved gas concentration were only measured in exp. 2. Dry matter intake was reduced upon acrylic acid supplementation. There were no significant effects of any treatments in any experiments on H2 emission, except for a decrease in hourly H2 emission rate (g/h) at 1 h after feeding in both experiments. In exp. 2, H2 headspace proportions increased with ACR-2 supplementation, whereas dissolved concentrations were unaffected. In exp. 1, cows on ACR-1 increased propionate proportion at 1 h after feeding. In exp. 2, both FUM-2 and ACR-2 increased rumen propionate proportion in the hours after feeding and dosing. There was no effect on rumen acetate for cows on PHL-2. There was a strong positive correlation between rumen dissolved CH4 and headspace CH4 (r = 0.84), whereas the equivalent correlation was weaker for H2 (r = 0.41). For the relationship between dissolved concentrations and emissions of CH4 and H2, there was a moderate positive correlation for CH4 (r = 0.54), whereas it was weak for H2 (r = 0.28) with zero slope. In conclusion, the results suggested that fumaric acid and acrylic acid to some extent was reduced to propionate without associative effects on measures for H2 redirection. Furthermore, phloroglucinol seemed not to be metabolized in the rumen in the present study, because no effects on rumen acetate or measures of H2 were observed. Changes in H2 headspace and emission may be a poor proxy for actual changes in the rumen fluid concentration of H2.
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Affiliation(s)
- Morten Maigaard
- Department of Animal and Veterinary Sciences, AU Viborg-Research Centre Foulum, Aarhus University, 8830 DK-Tjele, Denmark.
| | - Martin R Weisbjerg
- Department of Animal and Veterinary Sciences, AU Viborg-Research Centre Foulum, Aarhus University, 8830 DK-Tjele, Denmark
| | | | - Mogens Larsen
- Department of Animal and Veterinary Sciences, AU Viborg-Research Centre Foulum, Aarhus University, 8830 DK-Tjele, Denmark
| | - Freja Bylling Andersen
- Department of Animal and Veterinary Sciences, AU Viborg-Research Centre Foulum, Aarhus University, 8830 DK-Tjele, Denmark
| | - Peter Lund
- Department of Animal and Veterinary Sciences, AU Viborg-Research Centre Foulum, Aarhus University, 8830 DK-Tjele, Denmark
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Cui M, Wei Y, Tan J, Li T, Jiao X, Zhou Y. Biochemical investigations of polyphenol degradation enzymes in the phototrophic bacterium Rubrivivax gelatinosus. Biochem J 2023; 480:1753-1766. [PMID: 37903000 DOI: 10.1042/bcj20230387] [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: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is an important intermediate in the degradation of flavonoids and tannins by anaerobic bacteria. Recent studies have shed light on the enzymatic mechanism of phloroglucinol degradation in butyrate-forming anaerobic bacteria, including environmental and intestinal bacteria such as Clostridium and Flavonifractor sp. Phloroglucinol degradation gene clusters have also been identified in other metabolically diverse bacteria, although the polyphenol metabolism of these microorganisms remain largely unexplored. Here, we describe biochemical studies of polyphenol degradation enzymes found in the purple non-sulfur bacterium Rubrivivax gelatinosus IL144, an anaerobic photoheterotroph reported to utilize diverse organic compounds as carbon sources for growth. In addition to the phloroglucinol reductase and dihydrophloroglucinol cyclohydrolase that catalyze phloroglucinol degradation, we characterize a Mn2+-dependent phloretin hydrolase that catalyzes the cleavage of phloretin into phloroglucinol and phloretic acid. We also report a Mn2+-dependent decarboxylase (DeC) that catalyzes the reversible decarboxylation of 2,4,6-trihydroxybenzoate to form phloroglucinol. A bioinformatics search led to the identification of DeC homologs in diverse soil and gut bacteria, and biochemical studies of a DeC homolog from the human gut bacterium Flavonifractor plautii demonstrated that it is also a 2,4,6-trihydroxybenzoate decarboxylase. Our study expands the range of enzymatic mechanisms for phloroglucinol formation, and provides further biochemical insight into polyphenol metabolism in the anaerobic biosphere.
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Affiliation(s)
- Mengyu Cui
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Jason Tan
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
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Zhou Y, Wei Y, Jiang L, Jiao X, Zhang Y. Anaerobic phloroglucinol degradation by Clostridium scatologenes. mBio 2023; 14:e0109923. [PMID: 37341492 PMCID: PMC10470551 DOI: 10.1128/mbio.01099-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023] Open
Abstract
Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O2 requirement of phenol oxidases is thought to explain the microbial inertness of phenolic compounds in anoxic environments, such as peatlands, termed the enzyme latch hypothesis. A caveat of this model is that certain phenols are known to be degraded by strict anaerobic bacteria, although the biochemical basis for this process is incompletely understood. Here, we report the discovery and characterization of a gene cluster in the environmental bacterium Clostridium scatologenes for the degradation phloroglucinol (1,3,5-trihydroxybenzene), a key intermediate in the anaerobic degradation of flavonoids and tannins, which constitute the most abundant polyphenols in nature. The gene cluster encodes the key C-C cleavage enzyme dihydrophloroglucinol cyclohydrolase, as well as (S)-3-hydroxy-5-oxo-hexanoate dehydrogenase and triacetate acetoacetate-lyase, which enable phloroglucinol to be utilized as a carbon and energy source. Bioinformatics studies revealed the presence of this gene cluster in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on human health and carbon preservation in peat soils and other anaerobic environmental niches. IMPORTANCE This study provides novel insights into the microbiota's anaerobic metabolism of phloroglucinol, a critical intermediate in the degradation of polyphenols in plants. Elucidation of this anaerobic pathway reveals enzymatic mechanisms for the degradation of phloroglucinol into short-chain fatty acids and acetyl-CoA, which are used as a carbon and energy source for bacterium growth. Bioinformatics studies suggested the prevalence of this pathway in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on carbon preservation in peat soils and human gut health.
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Affiliation(s)
- Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Liu X, Hu YJ, Fan JH, Zhao J, Li S, Li CC. Recent synthetic studies towards natural products via [5 + 2] cycloaddition reactions. Org Chem Front 2018. [DOI: 10.1039/c7qo01123g] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this review, we provide a summary of recent progress regarding synthetic studies towards natural products via [5 + 2] cycloaddition reactions.
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Affiliation(s)
- Xin Liu
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
- Department of Chemistry
| | - Ya-Jian Hu
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
- Department of Chemistry
| | - Jian-Hong Fan
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
- Department of Chemistry
| | - Jing Zhao
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Shaoping Li
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Chuang-Chuang Li
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518055
- China
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7
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Ladino-Orjuela G, Gomes E, da Silva R, Salt C, Parsons JR. Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 237:105-121. [PMID: 26613990 DOI: 10.1007/978-3-319-23573-8_5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.
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Affiliation(s)
- Guillermo Ladino-Orjuela
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Eleni Gomes
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Roberto da Silva
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Christopher Salt
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
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Ellerbrock P, Armanino N, Ilg MK, Webster R, Trauner D. An eight-step synthesis of epicolactone reveals its biosynthetic origin. Nat Chem 2015; 7:879-82. [DOI: 10.1038/nchem.2336] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022]
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Brown CK, Vetting MW, Earhart CA, Ohlendorf DH. Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1. Annu Rev Microbiol 2004; 58:555-85. [PMID: 15487948 DOI: 10.1146/annurev.micro.57.030502.090927] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The catechol dioxygenases allow a wide variety of bacteria to use aromatic compounds as carbon sources by catalyzing the key ring-opening step. These enzymes use specifically either catechol or protocatechuate (2,3-dihydroxybenozate) as their substrates; they use a bare metal ion as the sole cofactor. To learn how this family of metalloenzymes functions, a structural analysis of designed and selected mutants of these enzymes has been undertaken. Here we review the results of this analysis on the nonheme ferric iron intradiol dioxygenase protocatechuate 3,4-dioxygenase.
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Affiliation(s)
- C Kent Brown
- Center for Metals in Biocatalysis and Department of Biochemistry, Molecular Biology, and Biophysics , Minneapolis, Minnesota 55455, USA.
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Kambourakis S, Draths KM, Frost JW. Synthesis of Gallic Acid and Pyrogallol from Glucose: Replacing Natural Product Isolation with Microbial Catalysis. J Am Chem Soc 2000. [DOI: 10.1021/ja000853r] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Spiros Kambourakis
- Departments of Chemistry and Chemical Engineering Michigan State University, East Lansing, Michigan 48824
| | - K. M. Draths
- Departments of Chemistry and Chemical Engineering Michigan State University, East Lansing, Michigan 48824
| | - J. W. Frost
- Departments of Chemistry and Chemical Engineering Michigan State University, East Lansing, Michigan 48824
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Vetting MW, D'Argenio DA, Ornston LN, Ohlendorf DH. Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry 2000; 39:7943-55. [PMID: 10891075 DOI: 10.1021/bi000151e] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases.
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Affiliation(s)
- M W Vetting
- Center of Metals in Biocatalysis and Department of Biochemistry, Molecular Biology and Biophysics, 6-155 Jackson Hall, 321 Church St. S.E., University of Minnesota Medical School, Minneapolis, Minnesota 55455-0347, USA
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