1
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Fang Y, Li X. Protein lysine four-carbon acylations in health and disease. J Cell Physiol 2024; 239:e30981. [PMID: 36815448 PMCID: PMC10704440 DOI: 10.1002/jcp.30981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
Lysine acylation, a type of posttranslational protein modification sensitive to cellular metabolic states, influences the functions of target proteins involved in diverse cellular processes. Particularly, lysine butyrylation, crotonylation, β-hydroxybutyrylation, and 2-hydroxyisobutyrylation, four types of four-carbon acylations, are modulated by intracellular concentrations of their respective acyl-CoAs and sensitive to alterations of nutrient metabolism induced by cellular and/or environmental signals. In this review, we discussed the metabolic pathways producing these four-carbon acyl-CoAs, the regulation of lysine acylation and deacylation, and the functions of individual lysine acylation.
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Affiliation(s)
- Yi Fang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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2
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Helbich S, Barrantes I, Dos Anjos Borges LG, Pieper DH, Vainshtein Y, Sohn K, Engesser KH. The 2-methylpropene degradation pathway in Mycobacteriaceae family strains. Environ Microbiol 2023; 25:2163-2181. [PMID: 37321960 DOI: 10.1111/1462-2920.16449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use 2-methylpropene (isobutene, 2-MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2-methylpropene derived from whole genome sequencing, differential expression analysis and peptide-mass fingerprinting. Key genes identified are coding for a 4-component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2-hydroxyisobutyryl-CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2-methylpropene degraders.
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Affiliation(s)
- Steffen Helbich
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Stuttgart, Germany
| | - Israel Barrantes
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Dietmar H Pieper
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yevhen Vainshtein
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Kai Sohn
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Karl-Heinrich Engesser
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Stuttgart, Germany
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3
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Chen Y, Ren H, Kong X, Wu H, Lu Z. A multicomponent propane monooxygenase catalyzes the initial degradation of methyl tert-butyl ether in Mycobacterium vaccae JOB5. Appl Environ Microbiol 2023; 89:e0118723. [PMID: 37823642 PMCID: PMC10617536 DOI: 10.1128/aem.01187-23] [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: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Methyl tert-butyl ether (MTBE) has been recognized as a groundwater contaminant due to its widespread distribution and potential threat to human health. The limited understanding of the enzymes catalyzing MTBE degradation restricts their application in MTBE bioremediation. In this study, an MTBE-degrading soluble di-iron monooxygenase that clusters phylogenetically with a known propane monooxygenase (PRM) encoded by the prmABCD gene cluster was identified and functionally characterized, revealing their role in MTBE metabolism by Mycobacterium vaccae JOB5. Transcriptome analysis demonstrated that the expression of prmABCD was upregulated when JOB5 was induced by MTBE. Escherichia coli Rosetta heterologously expressing prmABCD from JOB5 could transform MTBE, indicating that the PRM of JOB5 is capable of the initial degradation of MTBE. The loss of the gene encoding the oxygenase α-subunit or β-subunit, the coupling protein, or the reductase disrupted MTBE transformation by the recombinant E. coli Rosetta. In addition, the catalytic capacity of PRM is likely affected by residue G95 in the active site pocket and residues I84, P165, A269, and V270 in the substrate tunnel structure. Mutation of amino acids in the active site and substrate tunnel resulted in inefficiency or inactivation of MTBE degradation, and the activity in 1,4-dioxane (1,4-D) degradation was diminished less than that in MTBE degradation.IMPORTANCEMulticomponent monooxygenases catalyzing the initial hydroxylation of MTBE are important in MTBE biodegradation. Previous studies of MTBE degradation enzymes have focused on P450s, alkane monooxygenase and MTBE monooxygenase, but the vital role of soluble di-iron monooxygenases has rarely been reported. In this study, we deciphered the essential catalytic role of a PRM and revealed the key residues of the PRM in MTBE metabolism. Our findings provide new insight into the MTBE-degrading gene cluster and enzymes in bacteria. This characterization of the PRM associated with MTBE degradation expands our understanding of MTBE-degrading gene diversity and provides a novel candidate enzyme for the bioremediation of MTBE-contaminated sites.
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Affiliation(s)
- Yiyang Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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4
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Gunasekaran V, Canela N, Constantí M. Comparative Proteomic Analysis of an Ethyl Tert-Butyl Ether-Degrading Bacterial Consortium. Microorganisms 2022; 10:microorganisms10122331. [PMID: 36557584 PMCID: PMC9781318 DOI: 10.3390/microorganisms10122331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
A bacterial consortium capable of degrading ethyl tert-butyl ether (ETBE) as a sole carbon source was enriched and isolated from gasoline-contaminated water. Arthrobacter sp., Herbaspirillum sp., Pseudacidovorax sp., Pseudomonas sp., and Xanthomonas sp. were identified as the initial populations with the 16S rDNA analysis. The consortium aerobically degraded 49% of 50 mg/L of ETBE, in 6 days. The ETBE degrading efficiency of the consortium increased to 98% even with the higher concentrations of ETBE (1000 mg/L) in the subsequent subcultures, which accumulated tert-butyl alcohol (TBA). Xanthomonas sp. and Pseudomonas sp. were identified as the predominant ETBE degrading populations in the final subculture. The metaproteome of the ETBE-grown bacterial consortium was compared with the glucose-grown bacterial consortium, using 2D-DIGE. Proteins related to the ETBE metabolism, stress response, carbon metabolism and chaperones were found to be abundant in the presence of ETBE while proteins related to cell division were less abundant. The metaproteomic study revealed that the ETBE does have an effect on the metabolism of the bacterial consortium. It also enabled us to understand the responses of the complex bacterial consortium to ETBE, thus revealing interesting facts about the ETBE degrading bacterial community.
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Affiliation(s)
- Vijayalakshmi Gunasekaran
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans, 26, 43007 Tarragona, Spain
- FA Bio, Harpenden AL5 2JQ, UK
- Correspondence: (V.G.); (M.C.); Tel.: +34-977-558457 (M.C.)
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Av. Universitat 1, 43204 Reus, Spain
| | - Magda Constantí
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans, 26, 43007 Tarragona, Spain
- Correspondence: (V.G.); (M.C.); Tel.: +34-977-558457 (M.C.)
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5
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Isanapong J, Pornwongthong P. Immobilized laccase on zinc oxide nanoarray for catalytic degradation of tertiary butyl alcohol. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125104. [PMID: 33482503 DOI: 10.1016/j.jhazmat.2021.125104] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Laccase is an effective biocatalyst in bioremediation process; however, the application of the enzyme is limited due to its cost, recovery, and stability. In this study, we developed, characterized and evaluated the efficiency of immobilized laccase on zinc oxide nanostructure to catalyze biodegradation of TBA in comparison to the suspended enzyme. The results showed that both immobilized and suspended laccase were capable of catalyzing TBA biodegradation; however, the efficiency of the immobilized laccase on TBA removal was higher than that of the suspended enzyme. The repeatability testing revealed the potential of the immobilized laccase for repeatedly catalyzing TBA biodegradation with storage capacity. While the Vmax of immobilized enzyme was higher than suspended laccase (2.25 ± 0.542 mg TBA/h∙U vs. 1.47 ± 0.185 mg TBA/h∙U), the km of the immobilized enzyme was higher than the suspended laccase (67.9 ± 20.5 mg TBA/L vs. 33.5 ± 7.10 mg TBA/L). This suggests that the immobilized laccase is better in TBA removal, but has lower affinity with TBA than the suspended enzyme. Thus, immobilization of the enzyme can be applied to increase the efficiency and minimize the use of laccase for TBA remediation.
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Affiliation(s)
- Jantiya Isanapong
- Department of Agro-Industrial, Food and Environmental Technology, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok, Bangkok Thailand
| | - Peerapong Pornwongthong
- Department of Agro-Industrial, Food and Environmental Technology, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok, Bangkok Thailand.
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6
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Rohwerder T, Rohde MT, Jehmlich N, Purswani J. Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction. Front Microbiol 2020; 11:691. [PMID: 32351493 PMCID: PMC7176365 DOI: 10.3389/fmicb.2020.00691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/25/2020] [Indexed: 11/13/2022] Open
Abstract
The tertiary branched short-chain 2-hydroxyisobutyric acid (2-HIBA) has been associated with several metabolic diseases and lysine 2-hydroxyisobutyrylation seems to be a common eukaryotic as well as prokaryotic post-translational modification in proteins. In contrast, the underlying 2-HIBA metabolism has thus far only been detected in a few microorganisms, such as the betaproteobacterium Aquincola tertiaricarbonis L108 and the Bacillus group bacterium Kyrpidia tusciae DSM 2912. In these strains, 2-HIBA can be specifically activated to the corresponding CoA thioester by the 2-HIBA-CoA ligase (HCL) and is then isomerized to 3-hydroxybutyryl-CoA in a reversible and B12-dependent mutase reaction. Here, we demonstrate that the actinobacterial strain Actinomycetospora chiangmaiensis DSM 45062 degrades 2-HIBA and also its precursor 2-methylpropane-1,2-diol via acetone and formic acid by employing a thiamine pyrophosphate-dependent lyase. The corresponding gene is located directly upstream of hcl, which has previously been found only in operonic association with the 2-hydroxyisobutyryl-CoA mutase genes in other bacteria. Heterologous expression of the lyase gene from DSM 45062 in E. coli established a 2-hydroxyisobutyryl-CoA lyase activity in the latter. In line with this, analysis of the DSM 45062 proteome reveals a strong induction of the lyase-HCL gene cluster on 2-HIBA. Acetone is likely degraded via hydroxylation to acetol catalyzed by a MimABCD-related binuclear iron monooxygenase and formic acid appears to be oxidized to CO2 by selenium-dependent dehydrogenases. The presence of the lyase-HCL gene cluster in isoprene-degrading Rhodococcus strains and Pseudonocardia associated with tropical leafcutter ant species points to a role in degradation of biogenic short-chain ketones and highly branched organic compounds.
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Affiliation(s)
- Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Maria-Teresa Rohde
- Institut für Chemie - Biophysikalische Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jessica Purswani
- Institute of Water Research, University of Granada, Granada, Spain
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7
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Liang Z, Li G, Mai B, An T. Biodegradation of typical BFRs 2,4,6-tribromophenol by an indigenous strain Bacillus sp. GZT isolated from e-waste dismantling area through functional heterologous expression. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134159. [PMID: 31491624 DOI: 10.1016/j.scitotenv.2019.134159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Legacy wastewater contaminants from e-waste dismantling process such as 2,4,6-tribromophenol (TBP), one of the most widely used brominated flame retardants (BFRs), have raised concern owing to their toxicity and recalcitrance. Our previously isolated Bacillus sp. GZT from river sludge in e-waste dismantling area is a good candidate for bioremediation of BFRs contaminated sites considering its remarkable degradability of TBP and its intermediates. However, there exists a new challenge because bio-degrader cannot produce enough biomass or metabolic activity to cleanup TBP in practice complex environment. Here, we heterologously expressed and functionally characterized the genes and enzymes responsible for TBP degradation to examine the feasibility of enhancing the ability of this microorganism to detoxify TBP. Results demonstrated that five recombinant strains containing functional genes, designated tbpA, tbpB, tbpC, tbpD, and tbpE, become more tolerant toward a wide range of brominated compounds than the nontransgenic strain. Cytochrome P450 reductase encoded by tbpA gene could greatly increase efficiency to remove TBP (98.8%), as compared to wild-type strain GZT (93.2%). Its debromination intermediates 2,4-dibromophenol, 2,6-dibromo-4-methylphenol and 2-bromophenol were significantly metabolized by halophenol dehalogenases encoded by tbpB, tbpC, and tbpD, respectively. Finally, under the function of tbpE gene encoding enzyme, further debrominated product (phenol) was dramatically detoxified. To reduce the risk of these xenobiotics, the expression of these genes can be induced and significantly up-regulated during exposure to them. These results open broad scope for future study in developing genetic engineering technologies for more efficient remediation wastewater of e-waste recycling sites contaminated with TBP, which would certainly be important steps to lower TBP exposures and prevent potential health effects.
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Affiliation(s)
- Zhishu Liang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Bixian Mai
- State Key Laboratory of Organic Geochemistry, Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Taicheng An
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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8
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Huang H, Tang S, Ji M, Tang Z, Shimada M, Liu X, Qi S, Locasale JW, Roeder RG, Zhao Y, Li X. p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis. Mol Cell 2019; 70:663-678.e6. [PMID: 29775581 DOI: 10.1016/j.molcel.2018.04.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 12/25/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is an evolutionarily conserved and widespread histone mark like lysine acetylation (Kac). Here we report that p300 functions as a lysine 2-hyroxyisobutyryltransferase to regulate glycolysis in response to nutritional cues. We discovered that p300 differentially regulates Khib and Kac on distinct lysine sites, with only 6 of the 149 p300-targeted Khib sites overlapping with the 693 p300-targeted Kac sites. We demonstrate that diverse cellular proteins, particularly glycolytic enzymes, are targeted by p300 for Khib, but not for Kac. Specifically, deletion of p300 significantly reduces Khib levels on several p300-dependent, Khib-specific sites on key glycolytic enzymes including ENO1, decreasing their catalytic activities. Consequently, p300-deficient cells have impaired glycolysis and are hypersensitive to glucose-depletion-induced cell death. Our study reveals an p300-catalyzed, Khib-specific molecular mechanism that regulates cellular glucose metabolism and further indicate that p300 has an intrinsic ability to select short-chain acyl-CoA-dependent protein substrates.
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Affiliation(s)
- He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Shuang Tang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ming Ji
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shankang Qi
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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9
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Li S, Li D, Yan W. Cometabolism of methyl tert-butyl ether by a new microbial consortium ERS. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:10196-10205. [PMID: 25697553 DOI: 10.1007/s11356-015-4211-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
The release of methyl tert-butyl-ether (MTBE) into the environment has increased the worldwide concern about the pollution of MTBE. In this paper, a microbial consortium was isolated from the soil sample near an oil station, which can degrade MTBE directly with a low biomass yield and MTBE degrading efficiency. Further research has indicated that this consortium can degrade MTBE efficiently when grown on n-octane as the cometabolic substrate. The results of 16S rDNA based on phylogenetic analysis of the selected operating taxonomic units (OTUs) involved in the consortium revealed that one OTU was related to Pseudomonas putida GPo1, which could cometabolically degrade MTBE on the growth of n-octane. This may help explain why n-octane could be the optimal cometabolic substrate of the consortium for MTBE degradation. Furthermore, the degradation of MTBE was observed along with the consumption of n-octane. Different K s values for MTBE were observed for cells grown with or without n-octane, suggesting that different enzymes are responsible for the oxidation of MTBE in cells grown on n-octane or MTBE. The results are discussed in terms of their impacts on our understanding of MTBE biodegradation and cometabolism.
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Affiliation(s)
- Shanshan Li
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
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10
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Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium Mycobacterium sp. strain ELW1. Appl Environ Microbiol 2015; 81:1966-76. [PMID: 25576605 DOI: 10.1128/aem.03103-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An aerobic bacterium (Mycobacterium sp. strain ELW1) that utilizes 2-methylpropene (isobutylene) as a sole source of carbon and energy was isolated and characterized. Strain ELW1 grew on 2-methylpropene (growth rate = 0.05 h(-1)) with a yield of 0.38 mg (dry weight) mg 2-methylpropene(-1). Strain ELW1 also grew more slowly on both cis- and trans-2-butene but did not grow on any other C2 to C5 straight-chain, branched, or chlorinated alkenes tested. Resting 2-methylpropene-grown cells consumed ethene, propene, and 1-butene without a lag phase. Epoxyethane accumulated as the only detected product of ethene oxidation. Both alkene consumption and epoxyethane production were fully inhibited in cells exposed to 1-octyne, suggesting that alkene oxidation is initiated by an alkyne-sensitive, epoxide-generating monooxygenase. Kinetic analyses indicated that 1,2-epoxy-2-methylpropane is rapidly consumed during 2-methylpropene degradation, while 2-methyl-2-propen-1-ol is not a significant metabolite of 2-methylpropene catabolism. Degradation of 1,2-epoxy-2-methylpropane by 2-methylpropene-grown cells led to the accumulation and further degradation of 2-methyl-1,2-propanediol and 2-hydroxyisobutyrate, two sequential metabolites previously identified in the aerobic microbial metabolism of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA). Growth of strain ELW1 on 2-methylpropene, 1,2-epoxy-2-methylpropane, 2-methyl-1,2-propanediol, and 2-hydroxyisobutyrate was fully inhibited when cobalt ions were omitted from the growth medium, while growth on 3-hydroxybutyrate and other substrates was unaffected by the absence of added cobalt ions. Our results suggest that, like aerobic MTBE- and TBA-metabolizing bacteria, strain ELW1 utilizes a cobalt/cobalamin-dependent mutase to transform 2-hydroxyisobutyrate. Our results have been interpreted in terms of their impact on our understanding of the microbial metabolism of alkenes and ether oxygenates.
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11
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Auffret MD, Yergeau E, Labbé D, Fayolle-Guichard F, Greer CW. Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis. Appl Microbiol Biotechnol 2014; 99:2419-30. [PMID: 25343979 DOI: 10.1007/s00253-014-6159-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/12/2014] [Indexed: 11/29/2022]
Abstract
A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.
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Affiliation(s)
- Marc D Auffret
- Institut Français du Pétrole (IFP), 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France,
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12
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Biodegradation of fuel oxygenates and their effect on the expression of a newly identified cytochrome P450 gene in Achromobacter xylosoxidans MCM2/2/1. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.09.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer. Appl Microbiol Biotechnol 2013; 97:10531-9. [DOI: 10.1007/s00253-013-4803-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 11/26/2022]
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14
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Hyman M. Biodegradation of gasoline ether oxygenates. Curr Opin Biotechnol 2012; 24:443-50. [PMID: 23116604 DOI: 10.1016/j.copbio.2012.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 09/17/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
Abstract
Ether oxygenates such as methyl tertiary butyl ether (MTBE) are added to gasoline to improve fuel combustion and decrease exhaust emissions. Ether oxygenates and their tertiary alcohol metabolites are now an important group of groundwater pollutants. This review highlights recent advances in our understanding of the microorganisms, enzymes and pathways involved in both the aerobic and anaerobic biodegradation of these compounds. This review also aims to illustrate how these microbiological and biochemical studies have guided, and have helped refine, molecular and stable isotope-based analytical approaches that are increasingly being used to detect and quantify biodegradation of these compounds in contaminated environments.
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Affiliation(s)
- Michael Hyman
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA.
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Formation of alkenes via degradation of tert-alkyl ethers and alcohols by Aquincola tertiaricarbonis L108 and Methylibium spp. Appl Environ Microbiol 2011; 77:5981-7. [PMID: 21742915 DOI: 10.1128/aem.00093-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial degradation pathways of fuel oxygenates such as methyl tert-butyl and tert-amyl methyl ether (MTBE and TAME, respectively) have already been studied in some detail. However, many of the involved enzymes are still unknown, and possible side reactions have not yet been considered. In Aquincola tertiaricarbonis L108, Methylibium petroleiphilum PM1, and Methylibium sp. strain R8, we have now detected volatile hydrocarbons as by-products of the degradation of the tert-alkyl ether metabolites tert-butyl and tert-amyl alcohol (TBA and TAA, respectively). The alkene isobutene was formed only during TBA catabolism, while the beta and gamma isomers of isoamylene were produced only during TAA conversion. Both tert-alkyl alcohol degradation and alkene production were strictly oxygen dependent. However, the relative contribution of the dehydration reaction to total alcohol conversion increased with decreasing oxygen concentrations. In resting-cell experiments where the headspace oxygen content was adjusted to less than 2%, more than 50% of the TAA was converted to isoamylene. Isobutene formation from TBA was about 20-fold lower, reaching up to 4% alcohol turnover at low oxygen concentrations. It is likely that the putative tert-alkyl alcohol monooxygenase MdpJ, belonging to the Rieske nonheme mononuclear iron enzymes and found in all three strains tested, or an associated enzymatic step catalyzed the unusual elimination reaction. This was also supported by the detection of mdpJK genes in MTBE-degrading and isobutene-emitting enrichment cultures obtained from two treatment ponds operating at Leuna, Germany. The possible use of alkene formation as an easy-to-measure indicator of aerobic fuel oxygenate biodegradation in contaminated aquifers is discussed.
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Schäfer F, Breuer U, Benndorf D, von Bergen M, Harms H, Müller R. Growth ofAquincola tertiaricarbonis L108 ontert-Butyl Alcohol Leads to the Induction of a Phthalate Dioxygenase-related Protein and its Associated Oxidoreductase Subunit. Eng Life Sci 2007. [DOI: 10.1002/elsc.200700011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR. Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Appl Environ Microbiol 2007; 73:7347-57. [PMID: 17890343 PMCID: PMC2168209 DOI: 10.1128/aem.01604-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of tert-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in M. petroleiphilum PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.
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Affiliation(s)
- Krassimira R Hristova
- Department of Land Air and Water Resources, Plant and Environmental Sciences Building, University of California, Davis, Davis, CA 95616.
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Lopes Ferreira N, Mathis H, Labbé D, Monot F, Greer CW, Fayolle-Guichard F. n-Alkane assimilation and tert-butyl alcohol (TBA) oxidation capacity in Mycobacterium austroafricanum strains. Appl Microbiol Biotechnol 2007; 75:909-19. [PMID: 17347817 DOI: 10.1007/s00253-007-0892-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/09/2007] [Accepted: 02/11/2007] [Indexed: 11/27/2022]
Abstract
Mycobacterium austroafricanum IFP 2012, which grows on methyl tert-butyl ether (MTBE) and on tert-butyl alcohol (TBA), the main intermediate of MTBE degradation, also grows on a broad range of n-alkanes (C2 to C16). A single alkB gene copy, encoding a non-heme alkane monooxygenase, was partially amplified from the genome of this bacterium. Its expression was induced after growth on n-propane, n-hexane, n-hexadecane and on TBA but not after growth on LB. The capacity of other fast-growing mycobacteria to grow on n-alkanes (C1 to C16) and to degrade TBA after growth on n-alkanes was compared to that of M. austroafricanum IFP 2012. We studied M. austroafricanum IFP 2012 and IFP 2015 able to grow on MTBE, M. austroafricanum IFP 2173 able to grow on isooctane, Mycobacterium sp. IFP 2009 able to grow on ethyl tert-butyl ether (ETBE), M. vaccae JOB5 (M. austroaafricanum ATCC 29678) able to degrade MTBE and TBA and M. smegmatis mc2 155 with no known degradation capacity towards fuel oxygenates. The M. austroafricanum strains grew on a broad range of n-alkanes and three were able to degrade TBA after growth on propane, hexane and hexadecane. An alkB gene was partially amplified from the genome of all mycobacteria and a sequence comparison demonstrated a close relationship among the M. austroafricanum strains. This is the first report suggesting the involvement of an alkane hydroxylase in TBA oxidation, a key step during MTBE metabolism.
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Kane SR, Chakicherla AY, Chain PSG, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, Hristova KR. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 2007; 189:1931-45. [PMID: 17158667 PMCID: PMC1855728 DOI: 10.1128/jb.01259-06] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 11/29/2006] [Indexed: 11/20/2022] Open
Abstract
Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an approximately 4-Mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (approximately 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.
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Affiliation(s)
- Staci R Kane
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
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Müller RH, Rohwerder T, Harms H. Carbon conversion efficiency and limits of productive bacterial degradation of methyl tert-butyl ether and related compounds. Appl Environ Microbiol 2007; 73:1783-91. [PMID: 17220260 PMCID: PMC1828808 DOI: 10.1128/aem.01899-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The utilization of the fuel oxygenate methyl tert-butyl ether (MTBE) and related compounds by microorganisms was investigated in a mainly theoretical study based on the Y(ATP) concept. Experiments were conducted to derive realistic maintenance coefficients and K(s) values needed to calculate substrate fluxes available for biomass production. Aerobic substrate conversion and biomass synthesis were calculated for different putative pathways. The results suggest that MTBE is an effective heterotrophic substrate that can sustain growth yields of up to 0.87 g g(-1), which contradicts previous calculation results (N. Fortin et al., Environ. Microbiol. 3:407-416, 2001). Sufficient energy equivalents were generated in several of the potential assimilatory routes to incorporate carbon into biomass without the necessity to dissimilate additional substrate, efficient energy transduction provided. However, when a growth-related kinetic model was included, the limits of productive degradation became obvious. Depending on the maintenance coefficient m(s) and its associated biomass decay term b, growth-associated carbon conversion became strongly dependent on substrate fluxes. Due to slow degradation kinetics, the calculations predicted relatively high threshold concentrations, S(min), below which growth would not further be supported. S(min) strongly depended on the maximum growth rate mu(ma)(x), and b and was directly correlated with the half maximum rate-associated substrate concentration K(s), meaning that any effect impacting this parameter would also change S(min). The primary metabolic step, catalyzing the cleavage of the ether bond in MTBE, is likely to control the substrate flux in various strains. In addition, deficits in oxygen as an external factor and in reduction equivalents as a cellular variable in this reaction should further increase K(s) and S(min) for MTBE.
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Affiliation(s)
- Roland H Müller
- UFZ, Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, D-04318 Leipzig, Germany.
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Zhang RL, Huang GQ, Lian JY, Li XG. Degradation of MTBE and TBA by a new isolate from MTBE-contaminated soil. J Environ Sci (China) 2007; 19:1120-1124. [PMID: 17966519 DOI: 10.1016/s1001-0742(07)60182-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Methyl tert-butyl ether (MTBE), a gasoline additive, possesses serious problems to the environmental health. In the present study, a bacterial culture named A-3 which could effectively degrade MTBE was isolated from the MTBE contaminated soil. The isolate was identified as Chryseobacterium sp., a new species capable of degrading MTBE. In order to enhance its degradation ability, selected environment factors were investigated. The results showed that the optimal temperature was in the range of 25-30 degrees C, the pH was 7.0, the inoculum size was 2 x 10(8) CFU/ml and the optimal concentration of MTBE was from 50 to 100 mg/L. The maximum MTBE utilization rate (upsilon(max)) was 102 nmol MTBE/(mg cell protein x h). Furthermore, it was found that the isolate could also degrade tert-butyl alcohol (TBA). The degradation rates of TBA were much faster than those of MTBE. The additional TBA would lead to the decrease of the initial MTBE degradation rate and the inhibitory effect of TBA increased with the increase of TBA concentration. Similar protein profiles at least seven peptides were demonstrated after SDS-PAGE analysis of crude extracts obtained from the cells growing in MTBE and TBA culture.
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Affiliation(s)
- Rui-Ling Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Lopes Ferreira N, Malandain C, Fayolle-Guichard F. Enzymes and genes involved in the aerobic biodegradation of methyl tert-butyl ether (MTBE). Appl Microbiol Biotechnol 2006; 72:252-62. [PMID: 16804692 DOI: 10.1007/s00253-006-0494-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/04/2006] [Accepted: 05/04/2006] [Indexed: 10/24/2022]
Abstract
Fuel oxygenates, mainly methyl tert-butyl ether (MTBE) but also ethyl tert-butyl ether (ETBE), are added to gasoline in replacement of lead tetraethyl to enhance its octane index. Their addition also improves the combustion efficiency and therefore decreases the emission of pollutants (CO and hydrocarbons). On the other hand, MTBE, being highly soluble in water and recalcitrant to biodegradation, is a major pollutant of water in aquifers contaminated by MTBE-supplemented gasoline during accidental release. MTBE was shown to be degraded through cometabolic oxidation or to be used as a carbon and energy source by a few microorganisms. We have summarized the present state of knowledge about the microorganisms involved in MTBE degradation and the MTBE catabolic pathways. The role of the different enzymes is discussed as well as the rare and recent data concerning the genes encoding the enzymes involved in the MTBE pathway. The phylogeny of the microorganisms isolated for their capacity to grow on MTBE is also described.
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Affiliation(s)
- Nicolas Lopes Ferreira
- Biotechnology and Biomass Chemistry Department, Institut Français du Pétrole, 1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
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