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Gough AM, Parker AC, O'Bryan PJ, Whitehead TR, Roy S, Garcia BL, Hoffman PS, Jeffrey Smith C, Rocha ER. New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile. Microbiologyopen 2024; 13:e1429. [PMID: 39109824 PMCID: PMC11304471 DOI: 10.1002/mbo3.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.
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Affiliation(s)
- Andrea M. Gough
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Anita C. Parker
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | | | | | - Sourav Roy
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Brandon L. Garcia
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Paul S. Hoffman
- Department of Medicine, Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - C. Jeffrey Smith
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Edson R. Rocha
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
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Mojanaga OO, Acharya KR, Lloyd MD. Recombinant protein production for structural and kinetic studies: A case study using M. tuberculosis α-methylacyl-CoA racemase (MCR). Methods Enzymol 2023; 690:1-37. [PMID: 37858526 DOI: 10.1016/bs.mie.2023.07.001] [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] [Indexed: 10/21/2023]
Abstract
Modern drug discovery is a target-driven approach in which a particular protein such as an enzyme is implicated in the disease process. Commonly, small-molecule drugs are identified using screening, rational design, and structural biology approaches. Drug screening, testing and optimization is typically conducted in vitro, and copious amounts of protein are required. The advent of recombinant DNA technologies has resulted in a rise in proteins purified by affinity techniques, typically by incorporating an "affinity tag" at the N- or C-terminus. Use of these tagged proteins and affinity techniques comes with a host of issues. This chapter describes the production of an untagged enzyme, α-methylacyl-CoA racemase (MCR) from Mycobacterium tuberculosis, using a recombinant E. coli system. Purification of the enzyme on a 100 mg scale using tandem anion-exchange chromatographies (DEAE-sepharose and RESOURCE-Q columns), and size-exclusion chromatographies is described. A modified protocol allowing the purification of cationic proteins is also described, based on tandem cation-exchange chromatographies (using CM-sepharose and RESOURCE-S columns) and size-exclusion chromatographies. The resulting MCR protein is suitable for biochemical and structural biology applications. The described protocols have wide applicability to the purification of other recombinant proteins and enzymes without using affinity chromatography.
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Affiliation(s)
- Otsile O Mojanaga
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - K Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
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3
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Oleate Hydratase from Lactobacillus rhamnosus ATCC 53103: A FADH2-Dependent Enzyme with Remarkable Industrial Potential. Catalysts 2021. [DOI: 10.3390/catal11091051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Recently, we described the preparation of the recombinant oleate hydratase from Lactobacillus rhamnosus ATCC 53103. We observed that the purified C-terminal His-tagged enzyme was completely inactive and the catalytic activity was partially restored only in presence of a large amount of flavin adenine dinucleotide (FAD). In the present work, we assess that this hydratase in the presence of the reduced form of flavin adenine dinucleotide (FADH2) is at least one hundred times as active as in the presence of the same concentration of FAD. By means of two different biochemical processes, we demonstrated unambiguously that oleate hydratase from Lactobacillus rhamnosus ATCC 53103 is a FADH2-dependent enzyme. As a first relevant application of this discovery, we devised a preparative procedure for the stereoselective synthesis of (R)-10-hydroxystearic acid. Accordingly, the hydration of oleic acid (up to 50 g/L) is performed on a multigram scale using the recombinant hydratase and FADH2 generated in situ as cofactor. The produced (R)-10-hydroxystearic acid (ee > 97%) precipitates from the reaction solvent (water/glycerol/ethanol) and is conveniently recovered by simple filtration (>90% yield).
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Hagedoorn PL, Hollmann F, Hanefeld U. Novel oleate hydratases and potential biotechnological applications. Appl Microbiol Biotechnol 2021; 105:6159-6172. [PMID: 34350478 PMCID: PMC8403116 DOI: 10.1007/s00253-021-11465-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Abstract Oleate hydratase catalyses the addition of water to the CC double bond of oleic acid to produce (R)-10-hydroxystearic acid. The enzyme requires an FAD cofactor that functions to optimise the active site structure. A wide range of unsaturated fatty acids can be hydrated at the C10 and in some cases the C13 position. The substrate scope can be expanded using ‘decoy’ small carboxylic acids to convert small chain alkenes to secondary alcohols, albeit at low conversion rates. Systematic protein engineering and directed evolution to widen the substrate scope and increase the conversion rate is possible, supported by new high throughput screening assays that have been developed. Multi-enzyme cascades allow the formation of a wide range of products including keto-fatty acids, secondary alcohols, secondary amines and α,ω-dicarboxylic acids. Key points • Phylogenetically distinct oleate hydratases may exhibit mechanistic differences. • Protein engineering to improve productivity and substrate scope is possible. • Multi-enzymatic cascades greatly widen the product portfolio.
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Affiliation(s)
- Peter Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands.
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
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A Novel and Efficient Method for the Synthesis of Methyl (R)-10-Hydroxystearate and FAMEs from Sewage Scum. Catalysts 2021. [DOI: 10.3390/catal11060663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In this work, the transesterification of methyl estolides (ME) extracted from the lipid component present in the sewage scum was investigated. Methyl 10-(R)-hydroxystearate (Me-10-HSA) and Fatty Acid Methyl Esters (FAMEs) were obtained in a single step. A three-level and four factorial Box–Behnken experimental design were used to study the effects of methanol amounts, catalyst, temperature, and reaction time on the transesterification reaction using aluminum chloride hexahydrate (AlCl3·6H2O) or hydrochloric acid (HCl) as catalysts. AlCl3·6H2O was found quite active as well as conventional homogeneous acid catalysts as HCl. In both cases, a complete conversion of ME into Me-10-HSA and FAMEs was observed. The products were isolated, quantified, and fully characterized. At the end of the process, Me-10-HSA (32.3%wt) was purified through a chromatographic separation and analyzed by NMR. The high enantiomeric excess (ee > 92%) of the R-enantiomer isomer opens a new scenario for the valorization of sewage scum.
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Zhang GX, You ZN, Yu JM, Liu YY, Pan J, Xu JH, Li CX. Discovery and Engineering of a Novel Baeyer-Villiger Monooxygenase with High Normal Regioselectivity. Chembiochem 2020; 22:1190-1195. [PMID: 33205522 DOI: 10.1002/cbic.202000478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/12/2020] [Indexed: 11/07/2022]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are remarkable biocatalysts for the Baeyer-Villiger oxidation of ketones to generate esters or lactones. The regioselectivity of BVMOs is essential for determining the ratio of the two regioisomeric products ("normal" and "abnormal") when catalyzing asymmetric ketone substrates. Starting from a known normal-preferring BVMO sequence from Pseudomonas putida KT2440 (PpBVMO), a novel BVMO from Gordonia sihwensis (GsBVMO) with higher normal regioselectivity (up to 97/3) was identified. Furthermore, protein engineering increased the specificity constant (kcat /KM ) 8.9-fold to 484 s-1 mM-1 for 10-ketostearic acid derived from oleic acid. Consequently, by using the variant GsBVMOC308L as an efficient biocatalyst, 10-ketostearic acid was efficiently transformed into 9-(nonanoyloxy)nonanoic acid, with a space-time yield of 60.5 g L-1 d-1 . This study showed that the mutant with higher regioselectivity and catalytic efficiency could be applied to prepare medium-chain ω-hydroxy fatty acids through biotransformation of long-chain aliphatic keto acids derived from renewable plant oils.
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Affiliation(s)
- Guang-Xiang Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Zhi-Neng You
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jia-Mei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yuan-Yang Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China.,Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, P. R. China
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Zhang Y, Eser BE, Kristensen P, Guo Z. Fatty acid hydratase for value-added biotransformation: A review. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Zhang W, Lee JH, Younes SHH, Tonin F, Hagedoorn PL, Pichler H, Baeg Y, Park JB, Kourist R, Hollmann F. Photobiocatalytic synthesis of chiral secondary fatty alcohols from renewable unsaturated fatty acids. Nat Commun 2020; 11:2258. [PMID: 32382158 PMCID: PMC7206127 DOI: 10.1038/s41467-020-16099-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 04/09/2020] [Indexed: 12/03/2022] Open
Abstract
En route to a bio-based chemical industry, the conversion of fatty acids into building blocks is of particular interest. Enzymatic routes, occurring under mild conditions and excelling by intrinsic selectivity, are particularly attractive. Here we report photoenzymatic cascade reactions to transform unsaturated fatty acids into enantiomerically pure secondary fatty alcohols. In a first step the C=C-double bond is stereoselectively hydrated using oleate hydratases from Lactobacillus reuteri or Stenotrophomonas maltophilia. Also, dihydroxylation mediated by the 5,8-diol synthase from Aspergillus nidulans is demonstrated. The second step comprises decarboxylation of the intermediate hydroxy acids by the photoactivated decarboxylase from Chlorella variabilis NC64A. A broad range of (poly)unsaturated fatty acids can be transformed into enantiomerically pure fatty alcohols in a simple one-pot approach. Natural fatty acids are important starting materials in bio-based chemical production. Here, the authors developed a two-enzyme cascade to produce enantiomerically pure secondary fatty alcohols from natural unsaturated fatty acids in one pot.
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Affiliation(s)
- Wuyuan Zhang
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Jeong-Hoo Lee
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sabry H H Younes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Harald Pichler
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Yoonjin Baeg
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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Fatty Acid Hydratases: Versatile Catalysts to Access Hydroxy Fatty Acids in Efficient Syntheses of Industrial Interest. Catalysts 2020. [DOI: 10.3390/catal10030287] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The utilization of hydroxy fatty acids has gained more and more attention due to its applicability in many industrial building blocks that require it, for example, polymers or fragrances. Furthermore, hydroxy fatty acids are accessible from biorenewables, thus contributing to a more sustainable raw material basis for industrial chemicals. Therefore, a range of investigations were done on fatty acid hydratases (FAHs), since these enzymes catalyze the addition of water to an unsaturated fatty acid, thus providing an elegant route towards hydroxy-substituted fatty acids. Besides the discovery and characterization of fatty acid hydratases (FAHs), the design and optimization of syntheses with these enzymes, the implementation in elaborate cascades, and the improvement of these biocatalysts, by way of mutation in terms of the substrate scope, has been investigated. This mini-review focuses on the research done on process development using fatty acid hydratases as a catalyst. It is notable that biotransformations, running at impressive substrate loadings of up to 280 g L−1, have been realized. A further topic of this mini-review is the implementation of fatty acid hydratases in cascade reactions. In such cascades, fatty acid hydratases were, in particular, combined with alcohol dehydrogenases (ADH), Baeyer-Villiger monooxygenases (BVMO), transaminases (TA) and hydrolases, thus enabling access to a broad variety of molecules that are of industrial interest.
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10
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Wu YX, Pan J, Yu HL, Xu JH. Enzymatic synthesis of 10-oxostearic acid in high space-time yield via cascade reaction of a new oleate hydratase and an alcohol dehydrogenase. J Biotechnol 2019; 306S:100008. [DOI: 10.1016/j.btecx.2019.100008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 11/27/2022]
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Jeon EY, Song JW, Cha HJ, Lee SM, Lee J, Park JB. Intracellular transformation rates of fatty acids are influenced by expression of the fatty acid transporter FadL in Escherichia coli cell membrane. J Biotechnol 2018; 281:161-167. [DOI: 10.1016/j.jbiotec.2018.07.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 10/28/2022]
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Choi JH, Seo MJ, Lee KT, Oh DK. Biotransformation of fatty acid-rich tree oil hydrolysates to hydroxy fatty acid-rich hydrolysates by hydroxylases and their feasibility as biosurfactants. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-017-0374-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Complete genome sequence of Stenotrophomonas sp. KCTC 12332, a biotechnological potential bacterium. J Biotechnol 2017; 256:27-30. [DOI: 10.1016/j.jbiotec.2017.06.1207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 11/23/2022]
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14
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Comparison of Biochemical Properties of the Original and Newly Identified Oleate Hydratases from Stenotrophomonas maltophilia. Appl Environ Microbiol 2017; 83:AEM.03351-16. [PMID: 28235876 DOI: 10.1128/aem.03351-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/14/2017] [Indexed: 11/20/2022] Open
Abstract
Oleate hydratases (OhyAs) catalyze the conversion of unsaturated fatty acids to 10-hydroxy fatty acids, which are used as precursors of important industrial compounds, including lactones and ω-hydroxycarboxylic and α,ω-dicarboxylic acids. The genes encoding OhyA and a putative fatty acid hydratase in Stenotrophomonas maltophilia were identified by genomic analysis. The putative fatty acid hydratase was purified and identified as an oleate hydratase (OhyA2) based on its substrate specificity. The activity of OhyA2 as a holoenzyme was not affected by adding cofactors, whereas the activity of the original oleate hydratase (OhyA1) showed an increase. Thus, all characterized OhyAs were categorized as either OhyA1 or OhyA2 based on the activities of holoenzymes upon adding cofactors, which were determined by the type of the fourth conserved amino acid of flavin adenine dinucleotide (FAD)-binding motif. The hydration activities of S. maltophilia OhyA2 toward unsaturated fatty acids, including oleic acid, palmitoleic acid, linoleic acid, α-linolenic acid, and γ-linolenic acid, were greater than those of OhyA1. Moreover, the specific activity of S. maltophilia OhyA2 toward unsaturated fatty acids, with the exception of γ-linolenic acid, was the highest among all reported OhyAs.IMPORTANCE All characterized OhyAs were categorized as OhyA1s or OhyA2s based on the different properties of the reported and newly identified holo-OhyAs in S. maltophilia upon the addition of cofactors. OhyA2s showed higher activities toward polyunsaturated fatty acids (PUFAs), including linoleic acid, α-linolenic acid, and γ-linolenic acid, than those of OhyA1s. This suggests that OhyA2s can be used more effectively to convert plant oils to 10-hydroxy fatty acids because plant oils contain not only oleic acid but also PUFAs. The hydration activity of the newly identified OhyA2 from S. maltophilia toward oleic acid was the highest among the activity levels reported so far. Therefore, this enzyme is an efficient biocatalyst for the conversion of plant oils to 10-hydroxy fatty acids, which can be further converted to important industrial materials.
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