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Schroeter KL, Rolfe N, Forrester TJ, Kimber MS, Seah SY. Shy is a Proteobacterial steroid hydratase which catalyzes steroid side chain degradation without requiring a catalytically inert partner domain. J Biol Chem 2024:107509. [PMID: 38944126 DOI: 10.1016/j.jbc.2024.107509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024] Open
Abstract
Shy (side chain hydratase) and Sal (side chain aldolase), are involved in successive reactions in the pathway of bile acid side chain catabolism in Proteobacteria. Untagged Shy co-purified with His-tagged Sal indicating that the two enzymes form a complex. Shy contains a MaoC and a DUF35 domain. When co-expressed with Sal, the DUF35 domain but not the MaoC domain of Shy was observed to co-purify with Sal, indicating Sal interacts with Shy through its DUF35 domain. The MaoC domain of Shy (ShyMaoC) remained catalytically viable and could hydrate cholyl-enoyl-CoA with similar catalytic efficiency as in the Shy-Sal complex. Sal expressed with the DUF35 domain of Shy (Sal-ShyDUF35) was similarly competent for the retroaldol cleavage of cholyl-3-OH-CoA. ShyMaoC showed a preference for C5 side chain bile acid substrates, exhibiting low activity towards C3 side chain substrates. The ShyMaoC structure was determined by X-ray crystallography, showing a hot dog fold with a short central helix surrounded by a twisted anti-parallel β-sheet. Modeling and mutagenesis studies suggest that the bile acid substrate occupies the large open cleft formed by the truncated central helix and repositioning of the active site housing. ShyMaoC therefore contains two substrate binding sites per homodimer, making it distinct from previously characterized MaoC steroid hydratases that are (pseudo)-heterodimers with one substrate binding site per dimer. The characterization of Shy provides insight into how MaoC family hydratases have adapted to accommodate large polycyclic substrates that can facilitate future engineering of these enzymes to produce novel steroid pharmaceuticals.
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Affiliation(s)
- Kurt L Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Nicolas Rolfe
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | | | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Stephen Yk Seah
- Department of Molecular and Cellular Biology, University of Guelph, Canada.
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2
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Höing L, Sowa ST, Toplak M, Reinhardt JK, Jakob R, Maier T, Lill MA, Teufel R. Biosynthesis of the bacterial antibiotic 3,7-dihydroxytropolone through enzymatic salvaging of catabolic shunt products. Chem Sci 2024; 15:7749-7756. [PMID: 38784727 PMCID: PMC11110157 DOI: 10.1039/d4sc01715c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
The non-benzenoid aromatic tropone ring is a structural motif of numerous microbial and plant natural products with potent bioactivities. In bacteria, tropone biosynthesis involves early steps of the widespread CoA-dependent phenylacetic acid (paa) catabolon, from which a shunt product is sequestered and surprisingly further utilized as a universal precursor for structurally and functionally diverse tropone derivatives such as tropodithietic acid or (hydroxy)tropolones. Here, we elucidate the biosynthesis of the antibiotic 3,7-dihydroxytropolone in Actinobacteria by in vitro pathway reconstitution using paa catabolic enzymes as well as dedicated downstream tailoring enzymes, including a thioesterase (TrlF) and two flavoprotein monooxygenases (TrlCD and TrlE). We furthermore mechanistically and structurally characterize the multifunctional key enzyme TrlE, which mediates an unanticipated ipso-substitution involving a hydroxylation and subsequent decarboxylation of the CoA-freed side chain, followed by ring oxidation to afford tropolone. This study showcases a remarkably efficient strategy for 3,7-dihydroxytropolone biosynthesis and illuminates the functions of the involved biosynthetic enzymes.
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Affiliation(s)
- Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Sven T Sowa
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Marina Toplak
- Hilde-Mangold-Haus (CIBSS), University of Freiburg Habsburgerstrasse 49 79104 Freiburg im Breisgau Germany
| | - Jakob K Reinhardt
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Timm Maier
- Biozentrum, University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Zhang C, Xu Q, Fu J, Wu L, Li Y, Lu Y, Shi Y, Sun H, Li X, Wang L, Hong B. Engineering Streptomyces sp. CPCC 204095 for the targeted high-level production of isatropolone A by elucidating its pathway-specific regulatory mechanism. Microb Cell Fact 2024; 23:113. [PMID: 38622698 PMCID: PMC11020959 DOI: 10.1186/s12934-024-02387-0] [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: 02/06/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Isatropolone A and C, produced by Streptomyces sp. CPCC 204095, belong to an unusual class of non-benzenoid aromatic compounds and contain a rare seven-membered ring structure. Isatropolone A exhibits potent activity against Leishmania donovani, comparable to the only oral drug miltefosine. However, its variably low productivity represents a limitation for this lead compound in the future development of new anti-leishmaniasis drugs to meet unmet clinical needs. RESULTS Here we first elucidated the regulatory cascade of biosynthesis of isatropolones, which consists of two SARP family regulators, IsaF and IsaJ. Through a series of in vivo and in vitro experiments, IsaF was identified as a pathway-specific activator that orchestrates the transcription of the gene cluster essential for isatropolone biosynthesis. Interestingly, IsaJ was found to only upregulate the expression of the cytochrome P450 monooxygenase IsaS, which is crucial for the yield and proportion of isatropolone A and C. Through targeted gene deletions of isaJ or isaS, we effectively impeded the conversion of isatropolone A to C. Concurrently, the facilitation of isaF overexpression governed by selected promoters, prompted the comprehensive activation of the production of isatropolone A. Furthermore, meticulous optimization of the fermentation parameters was conducted. These strategies culminated in the attainment of an unprecedented maximum yield-980.8 mg/L of isatropolone A-achieved in small-scale solid-state fermentation utilizing the genetically modified strains, thereby establishing the highest reported titer to date. CONCLUSION In Streptomyces sp. CPCC 204095, the production of isatropolone A and C is modulated by the SARP regulators IsaF and IsaJ. IsaF serves as a master pathway-specific regulator for the production of isatropolones. IsaJ, on the other hand, only dictates the transcription of IsaS, the enzyme responsible for the conversion of isatropolone A and C. By engineering the expression of these pivotal genes, we have devised a strategy for genetic modification aimed at the selective and high-yield biosynthesis of isatropolone A. This study not only unveils the unique regulatory mechanisms governing isatropolone biosynthesis for the first time, but also establishes an essential engineering framework for the targeted high-level production of isatropolone A.
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Affiliation(s)
- Cong Zhang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qianqian Xu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jie Fu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Linzhuan Wu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuan Lu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Hongmin Sun
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xingxing Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Lifei Wang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Liu Y, Guo W, Wei C, Huang H, Nan F, Liu X, Liu Q, Lv J, Feng J, Xie S. Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis. ENVIRONMENTAL RESEARCH 2024; 246:118107. [PMID: 38181848 DOI: 10.1016/j.envres.2024.118107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.
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Affiliation(s)
- Yang Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Weinan Guo
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Caihua Wei
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Hanjie Huang
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Fangru Nan
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xudong Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Qi Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Junping Lv
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Jia Feng
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Shulian Xie
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China.
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Dong X, Wu S, Rao Z, Xiao Y, Long Y, Xie Z. Insight into the High-Efficiency Benzo(a)pyrene Degradation Ability of Pseudomonas benzopyrenica BaP3 and Its Application in the Complete Bioremediation of Benzo(a)pyrene. Int J Mol Sci 2023; 24:15323. [PMID: 37895002 PMCID: PMC10607497 DOI: 10.3390/ijms242015323] [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: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common carcinogens. Benzo(a)pyrene is one of the most difficult high-molecular-weight (HMW) PAHs to remove. Biodegradation has become an ideal method to eliminate PAH pollutants from the environment. The existing research is mostly limited to low-molecular-weight PAHs; there is little understanding of HMW PAHs, particularly benzo(a)pyrene. Research into the biodegradation of HMW PAHs contributes to the development of microbial metabolic mechanisms and also provides new systems for environmental treatments. Pseudomonas benzopyrenica BaP3 is a highly efficient benzo(a)pyrene-degrading strain that is isolated from soil samples, but its mechanism of degradation remains unknown. In this study, we aimed to clarify the high degradation efficiency mechanism of BaP3. The genes encoding Rhd1 and Rhd2 in strain BaP3 were characterized, and the results revealed that rhd1 was the critical factor for high degradation efficiency. Molecular docking and enzyme activity determinations confirmed this conclusion. A recombinant strain that could completely mineralize benzo(a)pyrene was also proposed for the first time. We explained the mechanism of the high-efficiency benzo(a)pyrene degradation ability of BaP3 to improve understanding of the degradation mechanism of highly toxic PAHs and to provide new solutions to practical applications via synthetic biology.
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Affiliation(s)
| | | | | | | | | | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (X.D.); (S.W.); (Z.R.); (Y.X.); (Y.L.)
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Wang P, Xiao Y, Gao D, Long Y, Xie Z. The Gene paaZ of the Phenylacetic Acid (PAA) Catabolic Pathway Branching Point and ech outside the PAA Catabolon Gene Cluster Are Synergistically Involved in the Biosynthesis of the Iron Scavenger 7-Hydroxytropolone in Pseudomonas donghuensis HYS. Int J Mol Sci 2023; 24:12632. [PMID: 37628812 PMCID: PMC10454607 DOI: 10.3390/ijms241612632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT's biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid (PAA) catabolon genes in cluster 2 are involved in the biosynthesis of 7-HT and that two genes, paaZ (orf13) and ech, are synergistically involved in the biosynthesis of 7-HT in P. donghuensis HYS. Firstly, gene knockout and a sole carbon experiment indicated that the genes orf17-21 (paaEDCBA) and orf26 (paaG) were involved in the biosynthesis of 7-HT and participated in the PAA catabolon pathway in P. donghuensis HYS; these genes were arranged in gene cluster 2 in P. donghuensis HYS. Interestingly, ORF13 was a homologous protein of PaaZ, but orf13 (paaZ) was not essential for the biosynthesis of 7-HT in P. donghuensis HYS. A genome-wide BLASTP search, including gene knockout, complemented assays, and site mutation, showed that the gene ech homologous to the ECH domain of orf13 (paaZ) is essential for the biosynthesis of 7-HT. Three key conserved residues of ech (Asp39, His44, and Gly62) were identified in P. donghuensis HYS. Furthermore, orf13 (paaZ) could not complement the role of ech in the production of 7-HT, and the single carbon experiment indicated that paaZ mainly participates in PAA catabolism. Overall, this study reveals a natural association between PAA catabolon and the biosynthesis of 7-HT in P. donghuensis HYS. These two genes have a synergistic effect and different functions: paaZ is mainly involved in the degradation of PAA, while ech is mainly related to the biosynthesis of 7-HT in P. donghuensis HYS. These findings complement our understanding of the mechanism of the biosynthesis of 7-HT in the genus Pseudomonas.
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Affiliation(s)
| | | | | | - Yan Long
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (P.W.); (Y.X.); (D.G.)
| | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (P.W.); (Y.X.); (D.G.)
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Wang Y, Zhang X, Lin Y, Lin H. The electron transport mechanism of downflow Leersia hexandra Swartz constructed wetland-microbial fuel cell when used to treat Cr(VI) and p-chlorophenol. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:37929-37945. [PMID: 36576625 DOI: 10.1007/s11356-022-24872-y] [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: 08/30/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Constructed wetland-microbial fuel cells are used to treat heavy metal and/or refractory organic wastewater. However, the electron transport mechanism of downflow Leersia hexandra constructed wetland-microbial fuel cells (DLCW-MFCs) is poorly understood when used to treat composite-polluted wastewater containing Cr(VI) and p-chlorophenol (4-CP) (C&P). In this study, metagenomics and in situ electrochemical techniques were used to investigate the electrochemical properties and the electricigens and their dominant gene functions. The DLCW-MFC was used to treat C&P and single-pollutant wastewater containing Cr(VI) (SC) and 4-CP (SP). The results showed that C&P had a higher current response and charge transfer capability and lower solution resistance plus charge transfer resistance. The anode bacteria solution of C&P contained more electron carriers (RF, FMN, FAD, CoQ10, and Cyt c). Metagenomic sequencing indicated that the total relative abundance of the microorganisms associated with electricity production (Desulfovibrio, Pseudomonas, Azospirillum, Nocardia, Microbacterium, Delftia, Geobacter, Acinetobacter, Bacillus, and Clostridium) was the highest in C&P (4.24%). However, Microbacterium was abundant in SP (0.12%), which exerted antagonistic effects on other electricigens. Among the 10 electricigens based on gene annotation, C&P had a higher overall relative abundance of the Unigene gene annotated to the KO pathway and CAZy level B compared with SC and SP, which were 1.31% and 0.582% respectively. Unigene153954 (ccmC), Unigene357497 (coxB), and Unigene1033667 (ubiG) were related to the electron carrier Cyt c, electron transfer, and CoQ biosynthesis, respectively. These were annotated to Desulfovibrio, Delftia, and Pseudomonas, respectively. Unigene161312 (AA1) used phenols and other substrates as electron donors and was annotated to Pseudomonas. Other functional carbohydrate enzyme genes (e.g., GT2, GT4, and GH31) used carbohydrates as donors and were annotated to other electricigens. This study provides a theoretical basis for electron transfer to promote the development of CW-MFCs.
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Affiliation(s)
- Yian Wang
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China
| | - Xuehong Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China
| | - Yi Lin
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China
| | - Hua Lin
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China.
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, 541000, Guilin, China.
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Koteska D, Marter P, Huang S, Pradella S, Petersen J, Schulz S. Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria. Chembiochem 2023; 24:e202200530. [PMID: 36416092 PMCID: PMC10107727 DOI: 10.1002/cbic.202200530] [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: 09/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
Volatiles released by the apicomplexan alga Chromera velia CCAP1602/1 and their associated bacteria have been investigated. A metagenome analysis allowed the identification of the most abundant heterotrophic bacteria of the phycosphere, but the isolation of additional strains showed that metagenomics underestimated the complexity of the algal microbiome, However, a culture-independent approach revealed the presence of a planctomycete that likely represents a novel bacterial family. We analysed algal and bacterial volatiles by open-system-stripping analysis (OSSA) on Tenax TA desorption tubes, followed by thermodesorption, cryofocusing and GC-MS-analysis. The analyses of the alga and the abundant bacterial strains Sphingopyxis litoris A01A-101, Algihabitans albus A01A-324, "Coraliitalea coralii" A01A-333 and Litoreibacter sp. A01A-347 revealed sulfur- and nitrogen-containing compounds, ketones, alcohols, aldehydes, aromatic compounds, amides and one lactone, as well as the typical algal products, apocarotenoids. The compounds were identified by gas chromatographic retention indices, comparison of mass spectra and syntheses of reference compounds. A major algal metabolite was 3,4,4-trimethylcyclopent-2-en-1-one, an apocarotenoid indicating the presence of carotenoids related to capsanthin, not reported from algae so far. A low overlap in volatiles bouquets between C. velia and the bacteria was found, and the xenic algal culture almost exclusively released algal components.
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Affiliation(s)
- Diana Koteska
- Institut für Organische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Pia Marter
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Sixing Huang
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Silke Pradella
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7B38124BraunschweigGermany
| | - Stefan Schulz
- Institut für Organische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
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9
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Zhang L, Toplak M, Saleem-Batcha R, Höing L, Jakob R, Jehmlich N, von Bergen M, Maier T, Teufel R. Bacterial Dehydrogenases Facilitate Oxidative Inactivation and Bioremediation of Chloramphenicol. Chembiochem 2023; 24:e202200632. [PMID: 36353978 DOI: 10.1002/cbic.202200632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/09/2022] [Indexed: 11/11/2022]
Abstract
Antimicrobial resistance represents a major threat to human health and knowledge of the underlying mechanisms is therefore vital. Here, we report the discovery and characterization of oxidoreductases that inactivate the broad-spectrum antibiotic chloramphenicol via dual oxidation of the C3-hydroxyl group. Accordingly, chloramphenicol oxidation either depends on standalone glucose-methanol-choline (GMC)-type flavoenzymes, or on additional aldehyde dehydrogenases that boost overall turnover. These enzymes also enable the inactivation of the chloramphenicol analogues thiamphenicol and azidamfenicol, but not of the C3-fluorinated florfenicol. Notably, distinct isofunctional enzymes can be found in Gram-positive (e. g., Streptomyces sp.) and Gram-negative (e. g., Sphingobium sp.) bacteria, which presumably evolved their selectivity for chloramphenicol independently based on phylogenetic analyses. Mechanistic and structural studies provide further insights into the catalytic mechanisms of these biotechnologically interesting enzymes, which, in sum, are both a curse and a blessing by contributing to the spread of antibiotic resistance as well as to the bioremediation of chloramphenicol.
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Affiliation(s)
- Lei Zhang
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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10
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Jiao M, He W, Ouyang Z, Shi Q, Wen Y. Progress in structural and functional study of the bacterial phenylacetic acid catabolic pathway, its role in pathogenicity and antibiotic resistance. Front Microbiol 2022; 13:964019. [PMID: 36160191 PMCID: PMC9493321 DOI: 10.3389/fmicb.2022.964019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Phenylacetic acid (PAA) is a central intermediate metabolite involved in bacterial degradation of aromatic components. The bacterial PAA pathway mainly contains 12 enzymes and a transcriptional regulator, which are involved in biofilm formation and antimicrobial activity. They are present in approximately 16% of the sequenced bacterial genome. In this review, we have summarized the PAA distribution in microbes, recent structural and functional study progress of the enzyme families of the bacterial PAA pathway, and their role in bacterial pathogenicity and antibiotic resistance. The enzymes of the bacterial PAA pathway have shown potential as an antimicrobial drug target for biotechnological applications in metabolic engineering.
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Affiliation(s)
- Min Jiao
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wenbo He
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Zhenlin Ouyang
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Qindong Shi
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Yurong Wen
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Yurong Wen,
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11
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Price MN, Deutschbauer AM, Arkin AP. Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PLoS Genet 2022; 18:e1010156. [PMID: 35417463 PMCID: PMC9007349 DOI: 10.1371/journal.pgen.1010156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/18/2022] [Indexed: 12/02/2022] Open
Abstract
To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind's predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.
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Affiliation(s)
- Morgan N. Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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12
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Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517774. [PMID: 35099011 PMCID: PMC9075582 DOI: 10.1093/femsre/fuac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.
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Affiliation(s)
| | | | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Lone Gram
- Corresponding author: Department of Bioechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark. Tel: +45 23688295; E-mail:
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13
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Toplak M, Teufel R. Three Rings to Rule Them All: How Versatile Flavoenzymes Orchestrate the Structural Diversification of Natural Products. Biochemistry 2021; 61:47-56. [PMID: 34962769 PMCID: PMC8772269 DOI: 10.1021/acs.biochem.1c00763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The structural diversification
of natural products is instrumental
to their versatile bioactivities. In this context, redox tailoring
enzymes are commonly involved in the modification and functionalization
of advanced pathway intermediates en route to the mature natural products.
In recent years, flavoprotein monooxygenases have been shown to mediate
numerous redox tailoring reactions that include not only (aromatic)
hydroxylation, Baeyer–Villiger oxidation, or epoxidation reactions
but also oxygenations that are coupled to extensive remodeling of
the carbon backbone, which are often central to the installment of
the respective pharmacophores. In this Perspective, we will highlight
recent developments and discoveries in the field of flavoenzyme catalysis
in bacterial natural product biosynthesis and illustrate how the flavin
cofactor can be fine-tuned to enable chemo-, regio-, and stereospecific
oxygenations via distinct flavin-C4a-peroxide and flavin-N5-(per)oxide
species. Open questions remain, e.g., regarding the breadth of chemical
reactions enabled particularly by the newly discovered flavin-N5-oxygen
adducts and the role of the protein environment in steering such cascade-like
reactions. Outstanding cases involving different flavin oxygenating
species will be exemplified by the tailoring of bacterial aromatic
polyketides, including enterocin, rubromycins, rishirilides, mithramycin,
anthracyclins, chartreusin, jadomycin, and xantholipin. In addition,
the biosynthesis of tropone natural products, including tropolone
and tropodithietic acid, will be presented, which features a recently
described prototypical flavoprotein dioxygenase that may combine flavin-N5-peroxide
and flavin-N5-oxide chemistry. Finally, structural and mechanistic
features of selected enzymes will be discussed as well as hurdles
for their application in the formation of natural product derivatives
via bioengineering.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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14
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Biosynthesis of Ditropolonyl Sulfide, an Antibacterial Compound Produced by Burkholderia cepacia Complex Strain R-12632. Appl Environ Microbiol 2021; 87:e0116921. [PMID: 34524894 DOI: 10.1128/aem.01169-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Burkholderia cepacia complex strain R-12632 produces ditropolonyl sulfide, an unusual sulfur-containing tropone, via a yet-unknown biosynthetic pathway. Ditropolonyl sulfide purified from a culture of strain R-12632 inhibits the growth of various Gram-positive and Gram-negative resistant bacteria, with MIC values as low as 16 μg/ml. In the present study, we used a transposon mutagenesis approach combined with metabolite analyses to identify the genetic basis for antibacterial activity of strain R-12632 against Gram-negative bacterial pathogens. Fifteen of the 8304 transposon mutants investigated completely lost antibacterial activity against Klebsiella pneumoniae LMG 2095. In these loss-of-activity mutants, nine genes were interrupted. Four of those genes were involved in assimilatory sulfate reduction, two were involved in phenylacetic acid (PAA) catabolism, and one was involved in glutathione metabolism. Via semipreparative fractionation and metabolite identification, it was confirmed that inactivation of the PAA degradation pathway or glutathione metabolism led to loss of ditropolonyl sulfide production. Based on earlier studies on the biosynthesis of tropolone compounds, the requirement for a functional PAA catabolic pathway for antibacterial activity in strain R-12632 indicated that this pathway likely provides the tropolone backbone for ditropolonyl sulfide. Loss of activity observed in mutants defective in assimilatory sulfate reduction and glutathione biosynthesis suggested that cysteine and glutathione are potential sources of the sulfur atom linking the two tropolone moieties. The demonstrated antibacterial activity of the unusual antibacterial compound ditropolonyl sulfide warrants further studies into its biosynthesis and biological role. IMPORTANCE Burkholderia bacteria are historically known for their biocontrol properties and have been proposed as a promising and underexplored source of bioactive specialized metabolites. Burkholderia cepacia complex strain R-12632 inhibits various Gram-positive and Gram-negative resistant pathogens and produces numerous specialized metabolites, among which is ditropolonyl sulfide. This unusual antimicrobial has been poorly studied and its biosynthetic pathway remains unknown. In the present study, we performed transposon mutagenesis of strain R-12632 and performed genome and metabolite analyses of loss-of-activity mutants to study the genetic basis for antibacterial activity. Our results indicate that phenylacetic acid catabolism, assimilatory sulfate reduction, and glutathione metabolism are necessary for ditropolonyl sulfide production. These findings contribute to understanding of the biosynthesis and biological role of this unusual antimicrobial.
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15
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Duan Y, Toplak M, Hou A, Brock NL, Dickschat JS, Teufel R. A Flavoprotein Dioxygenase Steers Bacterial Tropone Biosynthesis via Coenzyme A-Ester Oxygenolysis and Ring Epoxidation. J Am Chem Soc 2021; 143:10413-10421. [PMID: 34196542 PMCID: PMC8283759 DOI: 10.1021/jacs.1c04996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Bacterial tropone
natural products such as tropolone, tropodithietic
acid, or the roseobacticides play crucial roles in various terrestrial
and marine symbiotic interactions as virulence factors, antibiotics,
algaecides, or quorum sensing signals. We now show that their poorly
understood biosynthesis depends on a shunt product from aerobic CoA-dependent
phenylacetic acid catabolism that is salvaged by the dedicated acyl-CoA
dehydrogenase-like flavoenzyme TdaE. Further characterization of TdaE
revealed an unanticipated complex catalysis, comprising substrate
dehydrogenation, noncanonical CoA-ester oxygenolysis, and final ring
epoxidation. The enzyme thereby functions as an archetypal flavoprotein
dioxygenase that incorporates both oxygen atoms from O2 into the substrate, most likely involving flavin-N5-peroxide and
flavin-N5-oxide species for consecutive CoA-ester cleavage and epoxidation,
respectively. The subsequent spontaneous decarboxylation of the reactive
enzyme product yields tropolone, which serves as a key virulence factor
in rice panicle blight caused by pathogenic edaphic Burkholderia
plantarii. Alternatively, the TdaE product is most likely
converted to more complex sulfur-containing secondary metabolites
such as tropodithietic acid from predominant marine Rhodobacteraceae (e.g., Phaeobacter inhibens).
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Affiliation(s)
- Ying Duan
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Anwei Hou
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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16
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Marsh WS, Heise BW, Krzmarzick MJ, Murdoch RW, Fathepure BZ. Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water. Sci Rep 2021; 11:6943. [PMID: 33767228 PMCID: PMC7994583 DOI: 10.1038/s41598-021-86196-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.
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Affiliation(s)
- William S Marsh
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Brenden W Heise
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Mark J Krzmarzick
- Civil and Environmental Engineering, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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17
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Singha LP, Pandey P. Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil. Crit Rev Biotechnol 2021; 41:749-766. [PMID: 33626996 DOI: 10.1080/07388551.2021.1888066] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.
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Affiliation(s)
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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18
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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19
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Swarbrick CMD, Nanson JD, Patterson EI, Forwood JK. Structure, function, and regulation of thioesterases. Prog Lipid Res 2020; 79:101036. [PMID: 32416211 DOI: 10.1016/j.plipres.2020.101036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/15/2023]
Abstract
Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.
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Affiliation(s)
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward I Patterson
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales, Australia.
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20
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Spieker M, Saleem-Batcha R, Teufel R. Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism. ACS Chem Biol 2019; 14:2876-2886. [PMID: 31689071 DOI: 10.1021/acschembio.9b00742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous aromatic compounds are aerobically degraded in bacteria via the central intermediate phenylacetic acid (paa). In one of the key steps of this widespread catabolic pathway, 1,2-epoxyphenylacetyl-CoA is converted by PaaG into the heterocyclic oxepin-CoA. PaaG thereby elegantly generates an α,β-unsaturated CoA ester that is predisposed to undergo β-oxidation subsequent to hydrolytic ring-cleavage. Moreover, oxepin-CoA serves as a precursor for secondary metabolites (e.g., tropodithietic acid) that act as antibiotics and quorum-sensing signals. Here we verify that PaaG adopts a second role in aromatic catabolism by converting cis-3,4-didehydroadipoyl-CoA into trans-2,3-didehydroadipoyl-CoA and corroborate a Δ3,Δ2-enoyl-CoA isomerase-like proton shuttling mechanism for both distinct substrates. Biochemical and structural investigations of PaaG reveal active site adaptations to the structurally different substrates and provide detailed insight into catalysis and control of stereospecificity. This work elucidates the mechanism of action of unusual isomerase PaaG and sheds new light on the ubiquitous enoyl-CoA isomerases of the crotonase superfamily.
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Affiliation(s)
- Melanie Spieker
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Raspudin Saleem-Batcha
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Robin Teufel
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
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21
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Huang F, Li X, Guo J, Feng H, Yang F. Aromatic hydrocarbon compound degradation of phenylacetic acid by indigenous bacterial Sphingopyxis isolated from Lake Taihu. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2019; 82:1164-1171. [PMID: 31833448 DOI: 10.1080/15287394.2019.1703510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The aromatic compound phenylacetic acid (PAA) is present in the environment, and released in the catabolism of phenylalanine, 2-phenylethylamine, or environmental contaminants such as ethylbenzene and styrene. PAA was also proposed to be involved in human chronic kidney disease development. Several bacteria and fungi utilize these aromatic acids as sole carbon source either during aerobic or anaerobic conditions. The aromatic structure of PAA makes this compound resistant toward oxidation or reduction, because the stabilizing resonance energy of the aromatic ring system is difficult to overcome. In the case of bacteria that utilize aromatic compounds as growth substrates, the aromatic ring system limits survival due to a lack of carbon source. Sphingopyxis sp. YF1 isolated from Lake Taihu was found to be beneficial in bioremediation of aromatic compounds. This study thus aimed to examine the influence of environmental factors such as temperature, PAA concentration, and pH on the effectiveness of Sphingopyxis sp. YF1 to degrade aromatic compounds using PAA as model compound. Data showed the highest PAA-degrading rate of strain Sphingopyxis sp. YF1 was 7.6 mg/L·h under the condition of 20°C, pH 9 with a 1000 μg/ml concentration of PAA. Evidence indicates that PAA-degrading ability of strain Sphingopyxis sp. YF1 appears to be primarily influenced by the concentration of PAA, followed by temperature and pH. PAA-degrading gene PAAase was identified in this strain using polymerase chain reaction (PCR) method. These results illustrate that the bacteria Sphingopyxis sp. YF1 removes PAA effectively at certain environmental conditions and this proves beneficial in bioremediation of aromatic compounds.
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Affiliation(s)
- Feiyu Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xiaoyu Li
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jian Guo
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Hai Feng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
- Key laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Central South University, Changsha, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing, China
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22
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Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun 2019; 10:4127. [PMID: 31511507 PMCID: PMC6739347 DOI: 10.1038/s41467-019-11931-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2019] [Indexed: 02/06/2023] Open
Abstract
Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.
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Affiliation(s)
- Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Institute of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Giuseppe Cannone
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nainesh Katagihallimath
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Subramanian Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India.
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Li Y, Wang M, Zhao Q, Shen X, Wang J, Yan Y, Sun X, Yuan Q. Shunting Phenylacetic Acid Catabolism for Tropone Biosynthesis. ACS Synth Biol 2019; 8:876-883. [PMID: 30861343 DOI: 10.1021/acssynbio.9b00013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tropone is a seven-membered ring nonbenzenoid aromatic compound. It is the core structure of tropolonoids, which have various biological activities. In this study, a hybrid tropone biosynthetic pathway was designed by connecting phenylacetic acid (PAA) degradation with its biosynthesis and reconstituted in Escherichia coli. To simplify pathway construction and optimization, the use of E. coli endogenous genes was maximized and only three exogenous genes were employed. The entire pathway was divided into four modules: the endogenous shikimate pathway module, the hybrid PAA biosynthetic module, the endogenous PAA catabolic module and the heterogeneous tropone biosynthetic module. Efficiency of the PAA catabolic module was enhanced using PAA consumption rate as the indicator. Then, a single point mutation was introduced to inactivate the ALDH domain of PaaZ and the carbon flow was redirected toward tropone synthesis. Assembly of the full pathway led to de novo tropone production with the best titer of 65.2 ± 1.4 mg/L in shake flask experiment. This study provides a potential alternative for sustainable production of tropone and its derivatives.
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Affiliation(s)
- Yan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengyuan Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qianjing Zhao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Xinxiao Sun
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qipeng Yuan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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24
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Suvorova IA, Gelfand MS. Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria. Front Microbiol 2019; 10:642. [PMID: 30984152 PMCID: PMC6449761 DOI: 10.3389/fmicb.2019.00642] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 01/23/2023] Open
Abstract
Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), chlorocatechol (ClcR), methylcatechol (MmlR), 2,4-dichlorophenoxyacetate (TfdR, TfdS), phenol (AphS, AphR, AphT), biphenyl (BphS), and toluene (TbuT) metabolism. We characterize the complexity and variability in the organization of aromatic metabolism operons and the structure of regulatory networks that may differ even between closely related species. Generally, the upper parts of pathways, rare pathway variants, and degradative pathways of exotic and complex, in particular, xenobiotic compounds are often controlled by a single TF, while the regulation of more common and/or central parts of the aromatic metabolism may vary widely and often involves several TFs with shared and/or dual, or cascade regulation. The most frequent and at the same time variable connections exist between AphS, AphR, AphT, and BenR. We have identified a novel LysR-family TF that regulates the metabolism of catechol (or some catechol derivative) and either substitutes CatR(M)/BenM, or shares functions with it. We have also predicted several new members of aromatic metabolism regulons, in particular, some COGs regulated by several different TFs.
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Affiliation(s)
- Inna A Suvorova
- Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
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25
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Abstract
This review on natural products containing a tropolonoid motif highlights analytical methods applied for structural identification and biosynthetic pathway analysis, the ecological context and the pharmacological potential of this compound class.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
- 07745 Jena
- Germany
| | - David Roman
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
- 07745 Jena
- Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
- 07745 Jena
- Germany
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26
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Trautwein K, Hensler M, Wiegmann K, Skorubskaya E, Wöhlbrand L, Wünsch D, Hinrichs C, Feenders C, Müller C, Schell K, Ruppersberg H, Vagts J, Koßmehl S, Steinbüchel A, Schmidt-Kopplin P, Wilkes H, Hillebrand H, Blasius B, Schomburg D, Rabus R. The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. FEMS Microbiol Ecol 2018; 94:5074353. [PMID: 30124819 PMCID: PMC6122490 DOI: 10.1093/femsec/fiy154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/13/2018] [Indexed: 11/27/2022] Open
Abstract
Reduced nitrogen species are key nutrients for biological productivity in the oceans. Ammonium is often present in low and growth-limiting concentrations, albeit peaks occur during collapse of algal blooms or via input from deep sea upwelling and riverine inflow. Autotrophic phytoplankton exploit ammonium peaks by storing nitrogen intracellularly. In contrast, the strategy of heterotrophic bacterioplankton to acquire ammonium is less well understood. This study revealed the marine bacterium Phaeobacter inhibens DSM 17395, a Roseobacter group member, to have already depleted the external ammonium when only ∼⅓ of the ultimately attained biomass is formed. This was paralleled by a three-fold increase in cellular nitrogen levels and rapid buildup of various nitrogen-containing intracellular metabolites (and enzymes for their biosynthesis) and biopolymers (DNA, RNA and proteins). Moreover, nitrogen-rich cells secreted potential RTX proteins and the antibiotic tropodithietic acid, perhaps to competitively secure pulses of external ammonium and to protect themselves from predation. This complex response may ensure growing cells and their descendants exclusive provision with internal nitrogen stocks. This nutritional strategy appears prevalent also in other roseobacters from distant geographical provenances and could provide a new perspective on the distribution of reduced nitrogen in marine environments, i.e. temporary accumulation in bacterioplankton cells.
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Affiliation(s)
- Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Michael Hensler
- Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Rebenring 56, Braunschweig 38106, Germany
| | - Katharina Wiegmann
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Ekaterina Skorubskaya
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Constanze Müller
- Analytical BioGeoChemistry, HelmholtzZentrum München, German Research Centre for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Kristina Schell
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Hanna Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Jannes Vagts
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Sebastian Koßmehl
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Alexander Steinbüchel
- Institute for Molecular Microbiology and Biotechnology, WWU Münster, Corrensstr. 3, Münster 48149, Germany
| | - Philippe Schmidt-Kopplin
- Analytical BioGeoChemistry, HelmholtzZentrum München, German Research Centre for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Helmut Hillebrand
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, Oldenburg 23129, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
| | - Dietmar Schomburg
- Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Rebenring 56, Braunschweig 38106, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26111, Germany
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27
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Biosynthesis of Tropolones in Streptomyces spp.: Interweaving Biosynthesis and Degradation of Phenylacetic Acid and Hydroxylations on the Tropone Ring. Appl Environ Microbiol 2018; 84:AEM.00349-18. [PMID: 29654178 DOI: 10.1128/aem.00349-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/05/2018] [Indexed: 01/10/2023] Open
Abstract
Tropolonoids are important natural products that contain a unique seven-membered aromatic tropolone core and exhibit remarkable biological activities. 3,7-Dihydroxytropolone (DHT) isolated from Streptomyces species is a multiply hydroxylated tropolone exhibiting antimicrobial, anticancer, and antiviral activities. In this study, we determined the DHT biosynthetic pathway by heterologous expression, gene deletion, and biotransformation. Nine trl genes and some of the aerobic phenylacetic acid degradation pathway genes (paa) located outside the trl biosynthetic gene cluster are required for the heterologous production of DHT. The trlA gene encodes a single-domain protein homologous to the C-terminal enoyl coenzyme A (enoyl-CoA) hydratase domain of PaaZ. TrlA truncates the phenylacetic acid catabolic pathway and redirects it toward the formation of heptacyclic intermediates. TrlB is a 3-deoxy-d-arabino-heptulosonic acid-7-phosphate (DAHP) synthase homolog. TrlH is an unusual bifunctional protein bearing an N-terminal prephenate dehydratase domain and a C-terminal chorismate mutase domain. TrlB and TrlH enhanced de novo biosynthesis of phenylpyruvate, thereby providing abundant precursor for the prolific production of DHT in Streptomyces spp. Six seven-membered carbocyclic compounds were identified from the trlC, trlD, trlE, and trlF deletion mutants. Four of these chemicals, including 1,4,6-cycloheptatriene-1-carboxylic acid, tropone, tropolone, and 7-hydroxytropolone, were verified as key biosynthetic intermediates. TrlF is required for the conversion of 1,4,6-cycloheptatriene-1-carboxylic acid into tropone. The monooxygenases TrlE and TrlCD catalyze the regioselective hydroxylations of tropone to produce DHT. This study reveals a natural association of anabolism of chorismate and phenylpyruvate, catabolism of phenylacetic acid, and biosynthesis of tropolones in Streptomyces spp.IMPORTANCE Tropolonoids are promising drug lead compounds because of the versatile bioactivities attributed to their highly oxidized seven-membered aromatic ring scaffolds. Our present study provides clear insight into the biosynthesis of 3,7-dihydroxytropolone (DHT) through the identification of key genes responsible for the formation and modification of the seven-membered aromatic core. We also reveal the intrinsic mechanism of elevated production of DHT and related tropolonoids in Streptomyces spp. The study on DHT biosynthesis in Streptomyces exhibits a good example of antibiotic production in which both anabolic and catabolic pathways of primary metabolism are interwoven into the biosynthesis of secondary metabolites. Furthermore, our study sets the stage for metabolic engineering of the biosynthetic pathway for natural tropolonoid products and provides alternative synthetic biology tools for engineering novel tropolonoids.
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28
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Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation. 3 Biotech 2018; 8:118. [PMID: 29430379 PMCID: PMC5803133 DOI: 10.1007/s13205-018-1134-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.
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29
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Dickschat JS, Rinkel J, Klapschinski T, Petersen J. Characterisation of the l-Cystine β-Lyase PatB from Phaeobacter inhibens: An Enzyme Involved in the Biosynthesis of the Marine Antibiotic Tropodithietic Acid. Chembiochem 2017; 18:2260-2267. [PMID: 28895253 DOI: 10.1002/cbic.201700358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 01/22/2023]
Abstract
The l-cystine β-lyase from Phaeobacter inhibens is involved in the biosynthesis of the sulfur-containing antibiotic tropodithietic acid. The recombinant enzyme was obtained by heterologous expression in Escherichia coli and biochemically characterised by unambiguous chemical identification of the products formed from the substrate l-cystine, investigation of the substrate spectrum, determination of the enzyme kinetics, sequence alignment with closely related homologues and site-directed mutagenesis to identify a highly conserved lysine residue that is critical for functionality. PatB from P. inhibens is a new member of the small group of characterised l-cystine β-lyases and the first example of an enzyme with such an activity that is required for the biosynthesis of an antibiotic. A comparison of PatB to previously reported enzymes with l-cystine β-lyase activity from bacteria and plants is given.
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Affiliation(s)
- Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Tim Klapschinski
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, 38124, Braunschweig, Germany
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30
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Borjian F, Johnsen U, Schönheit P, Berg IA. Succinyl-CoA:Mesaconate CoA-Transferase and Mesaconyl-CoA Hydratase, Enzymes of the Methylaspartate Cycle in Haloarcula hispanica. Front Microbiol 2017; 8:1683. [PMID: 28932214 PMCID: PMC5592240 DOI: 10.3389/fmicb.2017.01683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/21/2017] [Indexed: 11/23/2022] Open
Abstract
Growth on acetate or other acetyl-CoA-generating substrates as a sole source of carbon requires an anaplerotic pathway for the conversion of acetyl-CoA into cellular building blocks. Haloarchaea (class Halobacteria) possess two different anaplerotic pathways, the classical glyoxylate cycle and the novel methylaspartate cycle. The methylaspartate cycle was discovered in Haloarcula spp. and operates in ∼40% of sequenced haloarchaea. In this cycle, condensation of one molecule of acetyl-CoA with oxaloacetate gives rise to citrate, which is further converted to 2-oxoglutarate and then to glutamate. The following glutamate rearrangement and deamination lead to mesaconate (methylfumarate) that needs to be activated to mesaconyl-C1-CoA and hydrated to β-methylmalyl-CoA. The cleavage of β-methylmalyl-CoA results in the formation of propionyl-CoA and glyoxylate. The carboxylation of propionyl-CoA and the condensation of glyoxylate with another acetyl-CoA molecule give rise to two C4-dicarboxylic acids, thus regenerating the initial acetyl-CoA acceptor and forming malate, its final product. Here we studied two enzymes of the methylaspartate cycle from Haloarcula hispanica, succinyl-CoA:mesaconate CoA-transferase (mesaconate CoA-transferase, Hah_1336) and mesaconyl-CoA hydratase (Hah_1340). Their genes were heterologously expressed in Haloferax volcanii, and the corresponding enzymes were purified and characterized. Mesaconate CoA-transferase was specific for its physiological substrates, mesaconate and succinyl-CoA, and produced only mesaconyl-C1-CoA and no mesaconyl-C4-CoA. Mesaconyl-CoA hydratase had a 3.5-fold bias for the physiological substrate, mesaconyl-C1-CoA, compared to mesaconyl-C4-CoA, and virtually no activity with other tested enoyl-CoA/3-hydroxyacyl-CoA compounds. Our results further prove the functioning of the methylaspartate cycle in haloarchaea and suggest that mesaconate CoA-transferase and mesaconyl-CoA hydratase can be regarded as characteristic enzymes of this cycle.
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Affiliation(s)
- Farshad Borjian
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität MünsterMünster, Germany.,Mikrobiologie, Fakultät für Biologie, Albert-Ludwigs-Universität FreiburgFreiburg, Germany
| | - Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu KielKiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu KielKiel, Germany
| | - Ivan A Berg
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität MünsterMünster, Germany.,Mikrobiologie, Fakultät für Biologie, Albert-Ludwigs-Universität FreiburgFreiburg, Germany
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31
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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32
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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Lightly TJ, Phung RR, Sorensen JL, Cardona ST. Synthetic cystic fibrosis sputum medium diminishes Burkholderia cenocepacia antifungal activity against Aspergillus fumigatus independently of phenylacetic acid production. Can J Microbiol 2017; 63:427-438. [PMID: 28178425 DOI: 10.1139/cjm-2016-0705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phenylacetic acid (PAA), an intermediate of phenylalanine degradation, is emerging as a signal molecule in microbial interactions with the host. In this work, we explore the presence of phenylalanine and PAA catabolism in 3 microbial pathogens of the cystic fibrosis (CF) lung microbiome: Pseudomonas aeruginosa, Burkholderia cenocepacia, and Aspergillus fumigatus. While in silico analysis of B. cenocepacia J2315 and A. fumigatus Af293 genome sequences showed complete pathways from phenylalanine to PAA, the P. aeruginosa PAO1 genome lacked several coding genes for phenylalanine and PAA catabolic enzymes. High-performance liquid chromatography analysis of supernatants from B. cenocepacia K56-2 detected PAA when grown in Luria-Bertani medium but not in synthetic cystic fibrosis sputum medium (SCFM). However, we were unable to identify PAA production by A. fumigatus or P. aeruginosa in any of the conditions tested. The inhibitory effect of B. cenocepacia on A. fumigatus growth was evaluated using agar plate interaction assays. Inhibition of fungal growth by B. cenocepacia was lessened in SCFM but this effect was not dependent on bacterial production of PAA. In summary, while we demonstrated PAA production by B. cenocepacia, we were not able to link this metabolite with the B. cenocepacia - A. fumigatus microbial interaction in CF nutritional conditions.
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Affiliation(s)
- Tasia Joy Lightly
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ryan R Phung
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - John L Sorensen
- b Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Silvia T Cardona
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,c Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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Groenhagen U, Leandrini De Oliveira AL, Fielding E, Moore BS, Schulz S. Coupled Biosynthesis of Volatiles and Salinosporamide A in Salinispora tropica. Chembiochem 2016; 17:1978-1985. [PMID: 27490971 DOI: 10.1002/cbic.201600388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Indexed: 02/06/2023]
Abstract
Terrestrial bacteria, especially actinomycetes, are known to be prolific producers of volatile compounds. We show here that bacteria from ocean sediments can also release complex bouquets of volatiles. The actinomycete Salinispora tropica produces cyclohexenyl compounds not previously known in nature, such as methyl cyclohex-2-ene-1-carboxylate (9), methyl 2-(cyclohex-2-en-1-yl)acetate (10), methyl (E/Z)-2-(cyclohex-2-en-1-ylidene)acetate (11/12), and related alcohols 8 and 13. These compounds were identified by GC/MS and confirmed by synthesis. In addition, rare spiroacetals, aromatic compounds, short-chain acids and esters, alcohols, and various cyclic compounds were produced by the bacteria. The biosynthesis of the cyclohexenyl compounds is closely coupled to that of cyclohexenylalanine (4), a building block of salinosporamide A, a proteasome inhibitor produced by S. tropica. Analysis of S. tropica strains that harbor knockouts of the salinosporamide biosynthetic genes salX and salD, coupled with feeding experiments, revealed that 3-(cyclohex-2-en-1-yl)-2-oxopropanoic acid (60) and 3-(cyclohex-2-en-1-ylidene)-2-oxopropanoic acid (isomers 61 and 62) are important intermediates in the biosynthesis of salinosporamide A, 4, and 8-13.
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Affiliation(s)
- Ulrike Groenhagen
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Ana Ligia Leandrini De Oliveira
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Elisha Fielding
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany.
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Investigation of the Genetics and Biochemistry of Roseobacticide Production in the Roseobacter Clade Bacterium Phaeobacter inhibens. mBio 2016; 7:e02118. [PMID: 27006458 PMCID: PMC4807370 DOI: 10.1128/mbio.02118-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Roseobacter clade bacteria are abundant in surface waters and are among the most metabolically diverse and ecologically significant species. This group includes opportunistic symbionts that associate with micro- and macroalgae. We have proposed that one representative member, Phaeobacter inhibens, engages in a dynamic symbiosis with the microalga Emiliania huxleyi. In one phase, mutualistically beneficial molecules are exchanged, including the Roseobacter-produced antibiotic tropodithietic acid (TDA), which is thought to protect the symbiotic interaction. In an alternative parasitic phase, triggered by algal senescence, the bacteria produce potent algaecides, the roseobacticides, which kill the algal host. Here, we employed genetic and biochemical screens to identify the roseobacticide biosynthetic gene cluster. By using a transposon mutagenesis approach, we found that genes required for TDA synthesis—the tda operon and paa catabolon—are also necessary for roseobacticide production. Thus, in contrast to the one-cluster–one-compound paradigm, the tda gene cluster can generate two sets of molecules with distinct structures and bioactivities. We further show that roseobacticide production is quorum sensing regulated via an N-acyl homoserine lactone signal (3-OH–C10-HSL). To ensure tight regulation of algaecide production, and thus of a lifestyle switch from mutualism to parasitism, roseobacticide biosynthesis necessitates the presence of both an algal senescence molecule and a quorum sensing signal. Marine Roseobacter species are abundant in the oceans and engage in symbiotic interactions with microscopic algae. One member, P. inhibens, produces the antibiotic TDA and a growth hormone thought to protect and promote algal growth. However, in the presence of molecules released by senescing algae, the bacteria produce potent algaecides, the roseobacticides, which kill the host. We examined the regulatory networks and biosynthetic genes required for roseobacticide production. We found that P. inhibens uses largely the same set of genes for production of both TDA and roseobacticides, thus providing a rare case in which one gene cluster synthesizes two structurally and functionally distinct molecules. Moreover, we found roseobacticide production to be regulated by quorum sensing. Thus, two small molecules, the algal metabolite and the quorum-sensing signal, ensure tight control in the production of roseobacticides. These results highlight the role of small molecules in regulating microbial symbioses.
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Hubrich F, Juneja P, Müller M, Diederichs K, Welte W, Andexer JN. Chorismatase Mechanisms Reveal Fundamentally Different Types of Reaction in a Single Conserved Protein Fold. J Am Chem Soc 2015; 137:11032-7. [DOI: 10.1021/jacs.5b05559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Hubrich
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
| | - Puneet Juneja
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Müller
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
| | - Kay Diederichs
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Wolfram Welte
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jennifer N. Andexer
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
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Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway. BIOLOGY 2015; 4:424-42. [PMID: 26075354 PMCID: PMC4498308 DOI: 10.3390/biology4020424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.
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Brock NL, Nikolay A, Dickschat JS. Biosynthesis of the antibiotic tropodithietic acid by the marine bacterium Phaeobacter inhibens. Chem Commun (Camb) 2015; 50:5487-9. [PMID: 24723119 DOI: 10.1039/c4cc01924e] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biosynthesis of tropodithietic acid was investigated using a combinatorial approach of feeding experiments, gene knockouts and bioinformatic analyses. The mechanism of sulfur introduction is distinct from known mechanisms in holomycin, thiomarinol A and gliotoxin biosynthesis.
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Affiliation(s)
- Nelson L Brock
- Institut für Organische Chemie, Hagenring 30, 38106 Braunschweig, Germany.
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Hattangady DS, Singh AK, Muthaiyan A, Jayaswal RK, Gustafson JE, Ulanov AV, Li Z, Wilkinson BJ, Pfeltz RF. Genomic, Transcriptomic and Metabolomic Studies of Two Well-Characterized, Laboratory-Derived Vancomycin-Intermediate Staphylococcus aureus Strains Derived from the Same Parent Strain. Antibiotics (Basel) 2015; 4:76-112. [PMID: 27025616 PMCID: PMC4790321 DOI: 10.3390/antibiotics4010076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/20/2014] [Accepted: 12/10/2014] [Indexed: 11/16/2022] Open
Abstract
Complete genome comparisons, transcriptomic and metabolomic studies were performed on two laboratory-selected, well-characterized vancomycin-intermediate Staphylococcus aureus (VISA) derived from the same parent MRSA that have changes in cell wall composition and decreased autolysis. A variety of mutations were found in the VISA, with more in strain 13136p(-)m⁺V20 (vancomycin MIC = 16 µg/mL) than strain 13136p(-)m⁺V5 (MIC = 8 µg/mL). Most of the mutations have not previously been associated with the VISA phenotype; some were associated with cell wall metabolism and many with stress responses, notably relating to DNA damage. The genomes and transcriptomes of the two VISA support the importance of gene expression regulation to the VISA phenotype. Similarities in overall transcriptomic and metabolomic data indicated that the VISA physiologic state includes elements of the stringent response, such as downregulation of protein and nucleotide synthesis, the pentose phosphate pathway and nutrient transport systems. Gene expression for secreted virulence determinants was generally downregulated, but was more variable for surface-associated virulence determinants, although capsule formation was clearly inhibited. The importance of activated stress response elements could be seen across all three analyses, as in the accumulation of osmoprotectant metabolites such as proline and glutamate. Concentrations of potential cell wall precursor amino acids and glucosamine were increased in the VISA strains. Polyamines were decreased in the VISA, which may facilitate the accrual of mutations. Overall, the studies confirm the wide variability in mutations and gene expression patterns that can lead to the VISA phenotype.
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Affiliation(s)
- Dipti S Hattangady
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Atul K Singh
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Arun Muthaiyan
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | | | - John E Gustafson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Alexander V Ulanov
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61807, USA.
| | - Zhong Li
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61807, USA.
| | - Brian J Wilkinson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Richard F Pfeltz
- BD Diagnostic Systems, Microbiology Research and Development, Sparks, MD 21152, USA.
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Pribytkova T, Lightly TJ, Kumar B, Bernier SP, Sorensen JL, Surette MG, Cardona ST. The attenuated virulence of aBurkholderia cenocepacia paaABCDEmutant is due to inhibition of quorum sensing by release of phenylacetic acid. Mol Microbiol 2014; 94:522-36. [DOI: 10.1111/mmi.12771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Tanya Pribytkova
- Department of Microbiology; University of Manitoba; Winnipeg Manitoba Canada
| | - Tasia Joy Lightly
- Department of Microbiology; University of Manitoba; Winnipeg Manitoba Canada
| | - Brijesh Kumar
- Department of Microbiology; University of Manitoba; Winnipeg Manitoba Canada
| | - Steve P. Bernier
- Department of Medicine; Farncombe Family Digestive Health Research Institute; McMaster University; Hamilton Ontario Canada
| | - John L. Sorensen
- Department of Chemistry; University of Manitoba; Winnipeg Manitoba Canada
| | - Michael G. Surette
- Department of Medicine; Farncombe Family Digestive Health Research Institute; McMaster University; Hamilton Ontario Canada
- Department of Biochemistry and Biological Sciences; McMaster University; Hamilton Ontario Canada
| | - Silvia T. Cardona
- Department of Microbiology; University of Manitoba; Winnipeg Manitoba Canada
- Department of Medical Microbiology & Infectious Disease; University of Manitoba; Winnipeg Manitoba Canada
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Rabe P, Klapschinski TA, Brock NL, Citron CA, D'Alvise P, Gram L, Dickschat JS. Synthesis and bioactivity of analogues of the marine antibiotic tropodithietic acid. Beilstein J Org Chem 2014; 10:1796-801. [PMID: 25161739 PMCID: PMC4142847 DOI: 10.3762/bjoc.10.188] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/22/2014] [Indexed: 01/24/2023] Open
Abstract
Tropodithietic acid (TDA) is a structurally unique sulfur-containing antibiotic from the Roseobacter clade bacterium Phaeobacter inhibens DSM 17395 and a few other related species. We have synthesised several structural analogues of TDA and used them in bioactivity tests against Staphylococcus aureus and Vibrio anguillarum for a structure–activity relationship (SAR) study, revealing that the sulfur-free analogue of TDA, tropone-2-carboxylic acid, has an antibiotic activity that is even stronger than the bioactivity of the natural product. The synthesis of this compound and of several analogues is presented and the bioactivity of the synthetic compounds is discussed.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Tim A Klapschinski
- Kekulé-Institut für Organische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Nelson L Brock
- Kekulé-Institut für Organische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Christian A Citron
- Kekulé-Institut für Organische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Paul D'Alvise
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg. 301, 2800 Kongens Lyngby, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg. 301, 2800 Kongens Lyngby, Denmark
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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Ismail W, El-Sayed WS. Degradation of phenylacetate by Acinetobacter spp.: evidence for the phenylacetyl-coenzyme A pathway. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0608-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Zimmermann M, Thormann V, Sauer U, Zamboni N. Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry. Anal Chem 2013; 85:8284-90. [PMID: 23895734 DOI: 10.1021/ac401555n] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coenzyme A (CoA) thioesters are ubiquitously present in metabolic networks and play a pivotal role in enzymatic formation and cleavage of carbon-carbon bonds. We present a method allowing nontargeted profiling of CoA-thioesters in biological samples. The reported UHPLC-MS/MS approach employes ion-pairing chromatography to separate CoA-metabolites carrying different chemical functionalities such as hydroxyl or multiple carboxyl groups and to distinguish between isomers. Selective detection of CoA-thioesters is accomplished by precursor ion scanning on a triple quadrupole mass spectrometer and takes advantage of the abundant fragment with m/z = -408 that originates from the CoA-moiety. We used a mixture of 19 commercially available CoA-derivatives to develop and optimize our method. As a proof of concept we demonstrated detection of the major CoA-intermediates of branched chain amino acid degradation in biological samples. We then applied our method to investigate degradation of lipids in the microorganism Mycobacterium smegmatis. Profiling of CoA-thioesters led to the discovery of a novel intermediate of cholesterol degradation. This demonstrates the power of our method for untargeted profiling of CoA-thioesters and adds a missing link in mycobacterial cholesterol catabolism.
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Affiliation(s)
- Michael Zimmermann
- Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland
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Has the bacterial biphenyl catabolic pathway evolved primarily to degrade biphenyl? The diphenylmethane case. J Bacteriol 2013; 195:3563-74. [PMID: 23749969 DOI: 10.1128/jb.00161-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we have compared the ability of Pandoraea pnomenusa B356 and of Burkholderia xenovorans LB400 to metabolize diphenylmethane and benzophenone, two biphenyl analogs in which the phenyl rings are bonded to a single carbon. Both chemicals are of environmental concern. P. pnomenusa B356 grew well on diphenylmethane. On the basis of growth kinetics analyses, diphenylmethane and biphenyl were shown to induce the same catabolic pathway. The profile of metabolites produced during growth of strain B356 on diphenylmethane was the same as the one produced by isolated enzymes of the biphenyl catabolic pathway acting individually or in coupled reactions. The biphenyl dioxygenase oxidizes diphenylmethane to 3-benzylcyclohexa-3,5-diene-1,2-diol very efficiently, and ultimately this metabolite is transformed to phenylacetic acid, which is further metabolized by a lower pathway. Strain B356 was also able to cometabolize benzophenone through its biphenyl pathway, although in this case, this substrate was unable to induce the biphenyl catabolic pathway and the degradation was incomplete, with accumulation of 2-hydroxy-6,7-dioxo-7-phenylheptanoic acid. Unlike strain B356, B. xenovorans LB400 did not grow on diphenylmethane. Its biphenyl pathway enzymes metabolized diphenylmethane, but they poorly metabolize benzophenone. The fact that the biphenyl catabolic pathway of strain B356 metabolized diphenylmethane and benzophenone more efficiently than that of strain LB400 brings us to postulate that in strain B356, this pathway evolved divergently to serve other functions not related to biphenyl degradation.
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Díaz E, Jiménez JI, Nogales J. Aerobic degradation of aromatic compounds. Curr Opin Biotechnol 2013; 24:431-42. [DOI: 10.1016/j.copbio.2012.10.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/04/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]
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Citron CA, Rabe P, Dickschat JS. The scent of bacteria: headspace analysis for the discovery of natural products. JOURNAL OF NATURAL PRODUCTS 2012; 75:1765-1776. [PMID: 22994159 DOI: 10.1021/np300468h] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Volatile compounds released by 50 bacterial strains, 45 of them actinobacteria in addition to three chloroflexi and two myxobacteria, have been collected by use of a closed-loop stripping apparatus, and the obtained headspace extracts have been analyzed by GC-MS. Excluding terpenes that have recently been published elsewhere, 254 compounds from all kinds of compound classes have been identified. For unambiguous compound identification several reference compounds have been synthesized. Among the detected volatiles 12 new natural products have been found, in addition to mellein, which was released by Saccharopolyspora erythraea. The iterative PKS for this compound has recently been identified by in vitro experiments, but mellein production in S. erythraea has never been reported before. These examples demonstrate that headspace analysis is an important tool for the discovery of natural products that may be overlooked using conventional techniques. The method is also useful for feeding experiments with isotopically labeled precursors and was applied to investigate the biosynthesis of the unusual nitrogen compound 1-nitro-2-methylpropane, which arises from valine. Furthermore, several streptomycetes emitted compounds that were previously recognized as insect pheromones, thus questioning if bacterial symbionts are involved in insect communication.
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Affiliation(s)
- Christian A Citron
- Institute of Organic Chemistry, Technical University of Braunschweig , Hagenring 30, 38106 Braunschweig, Germany
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47
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Riclea R, Aigle B, Leblond P, Schoenian I, Spiteller D, Dickschat JS. Volatile Lactones from Streptomycetes Arise via the Antimycin Biosynthetic Pathway. Chembiochem 2012; 13:1635-44. [DOI: 10.1002/cbic.201200260] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Indexed: 11/11/2022]
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Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M, Thomas T, Brinkhoff T. Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME JOURNAL 2012; 6:2229-44. [PMID: 22717884 DOI: 10.1038/ismej.2012.62] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.
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Affiliation(s)
- Sebastian Thole
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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49
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Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum. Appl Environ Microbiol 2012; 78:5796-804. [PMID: 22685150 DOI: 10.1128/aem.01588-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The industrially important organism Corynebacterium glutamicum has been characterized in recent years for its robust ability to assimilate aromatic compounds. In this study, C. glutamicum strain AS 1.542 was investigated for its ability to catabolize phenylacetic acid (PAA). The paa genes were identified; they are organized as a continuous paa gene cluster. The type strain of C. glutamicum, ATCC 13032, is not able to catabolize PAA, but the recombinant strain ATCC 13032/pEC-K18mob2::paa gained the ability to grow on PAA. The paaR gene, encoding a TetR family transcription regulator, was studied in detail. Disruption of paaR in strain AS 1.542 resulted in transcriptional increases of all paa genes. Transcription start sites and putative promoter regions were determined. An imperfect palindromic motif (5'-ACTNACCGNNCGNNCGGTNAGT-3'; 22 bp) was identified in the upstream regions of paa genes. Electrophoretic mobility shift assays (EMSA) demonstrated specific binding of PaaR to this motif, and phenylacetyl coenzyme A (PA-CoA) blocked binding. It was concluded that PaaR is the negative regulator of PAA degradation and that PA-CoA is the PaaR effector. In addition, GlxR binding sites were found, and binding to GlxR was confirmed. Therefore, PAA catabolism in C. glutamicum is regulated by the pathway-specific repressor PaaR, and also likely by the global transcription regulator GlxR. By comparative genomic analysis, we reconstructed orthologous PaaR regulons in 57 species, including species of Actinobacteria, Proteobacteria, and Flavobacteria, that carry PAA utilization genes and operate by conserved binding motifs, suggesting that PaaR-like regulation might commonly exist in these bacteria.
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Epoxy Coenzyme A Thioester pathways for degradation of aromatic compounds. Appl Environ Microbiol 2012; 78:5043-51. [PMID: 22582071 DOI: 10.1128/aem.00633-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aromatic compounds (biogenic and anthropogenic) are abundant in the biosphere. Some of them are well-known environmental pollutants. Although the aromatic nucleus is relatively recalcitrant, microorganisms have developed various catabolic routes that enable complete biodegradation of aromatic compounds. The adopted degradation pathways depend on the availability of oxygen. Under oxic conditions, microorganisms utilize oxygen as a cosubstrate to activate and cleave the aromatic ring. In contrast, under anoxic conditions, the aromatic compounds are transformed to coenzyme A (CoA) thioesters followed by energy-consuming reduction of the ring. Eventually, the dearomatized ring is opened via a hydrolytic mechanism. Recently, novel catabolic pathways for the aerobic degradation of aromatic compounds were elucidated that differ significantly from the established catabolic routes. The new pathways were investigated in detail for the aerobic bacterial degradation of benzoate and phenylacetate. In both cases, the pathway is initiated by transforming the substrate to a CoA thioester and all the intermediates are bound by CoA. The subsequent reactions involve epoxidation of the aromatic ring followed by hydrolytic ring cleavage. Here we discuss the novel pathways, with a particular focus on their unique features and occurrence as well as ecological significance.
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