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Willemin MS, Armand F, Hamelin R, Maillard J, Holliger C. Conditional essentiality of the 11-subunit complex I-like enzyme in strict anaerobes: the case of Desulfitobacterium hafniense strain DCB-2. Front Microbiol 2024; 15:1388961. [PMID: 38993499 PMCID: PMC11238625 DOI: 10.3389/fmicb.2024.1388961] [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: 02/20/2024] [Accepted: 05/28/2024] [Indexed: 07/13/2024] Open
Abstract
In oxidative phosphorylation, respiratory complex I serves as an entry point in the electron transport chain for electrons generated in catabolic processes in the form of NADH. An ancestral version of the complex, lacking the NADH-oxidising module, is encoded in a significant number of bacterial genomes. Amongst them is Desulfitobacterium hafniense, a strict anaerobe capable of conserving energy via organohalide respiration. This study investigates the role of the complex I-like enzyme in D. hafniense energy metabolism using rotenone as a specific complex I inhibitor under different growth conditions. The investigation revealed that the complex I-like enzyme was essential for growth with lactate and pyruvate but not in conditions involving H2 as an electron donor. In addition, a previously published proteomic dataset of strain DCB-2 was analysed to reveal the predominance of the complex under different growth conditions and to identify potential redox partners. This approach revealed seven candidates with expression patterns similar to Nuo homologues, suggesting the use of diverse electron sources. Based on these results, we propose a model where the complex I-like enzyme serves as an electron entry point into the respiratory chain for substrates delivering electrons within the cytoplasm, such as lactate or pyruvate, with ferredoxins shuttling electrons to the complex.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Armand
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Hamelin
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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2
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Cao D, Chen X, Nan J, Wang A, Li Z. Biomolecular insights into the inhibition of heavy metals on reductive dechlorination of 2,4,6-trichlorophenol in Pseudomonas sp. CP-1. WATER RESEARCH 2023; 247:120836. [PMID: 37950953 DOI: 10.1016/j.watres.2023.120836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023]
Abstract
Influences of heavy metal exposure to the organohalide respiration process and the related molecular mechanism remain poorly understood. In this study, a non-obligate organohalide respiring bacterium, Pseudomonas sp. strain CP-1, was isolated and its molecular response to the five types of commonly existed heavy metal ions were thoroughly investigated. All types of heavy metal ions posed inhibitory effects on 2,4,6-trichlorophenol dechlorination activity and cell growth with the varied degree. Exposure to Cu (II) showed the most serious inhibitive effects on dechlorination even at the lowest concentration of 0.05 mg/L, while the inhibition by As (V) was the least with the removal kinetic constant k decreased to 0.05 under 50 mg/L. Further, multi-omics analysis found compared with Cu (II), As (V) exposure led to the insignificant downregulation of a variety of biosynthesis processes, which would be one possible account for the less inhibited activity. More importantly, the inhibited mechanisms on the organohalide respiration catabolism of strain CP-1 were firstly revealed. Cu (II) stress severely downregulated NADH generation during TCA cycle and electron donation of organohalide respiration process, which might decrease the reducing power required for organohalide respiration. While both Cu (II) and As (Ⅴ) inhibited substrate level phosphorylation during TCA cycle, as well as electron transfer and ATP generation during organohalide respiration. Meanwhile, CprA-2 was confirmed as the responsible reductive dehalogenase in charge of 2,4,6-TCP dechlorination, and transcriptional and proteomic studies confirmed the directly inhibited gene transcription and expression of CprA-2. The in-depth reveal of inhibitory effects and mechanism gave theoretical supports for alleviating heavy metal inhibition on organohalide respiration activity in groundwater co-contaminated with organohalides and heavy metals.
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Affiliation(s)
- Di Cao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Xueqi Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
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Cimmino L, Duarte AG, Ni D, Ekundayo BE, Pereira IAC, Stahlberg H, Holliger C, Maillard J. Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun 2023; 14:7038. [PMID: 37923808 PMCID: PMC10624902 DOI: 10.1038/s41467-023-42927-7] [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: 06/24/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA2B2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Babatunde E Ekundayo
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Deng Z, Chen H, Wang J, Zhang N, Han Z, Xie Y, Zhang X, Fang X, Yu H, Zhang D, Yue Z, Zhang C. Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37478352 DOI: 10.1021/acs.est.3c03738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Haixin Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Jun Wang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Zhiqiang Han
- Department of Marine Resources and Environment, Fishery College, Zhejiang Ocean University, Zhoushan 316002, Zhejiang, China
| | - Yeting Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | - Xiaoyan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
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Yu Y, Zhang Y, Liu Y, Lv M, Wang Z, Wen LL, Li A. In situ reductive dehalogenation of groundwater driven by innovative organic carbon source materials: Insights into the organohalide-respiratory electron transport chain. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131243. [PMID: 36989787 DOI: 10.1016/j.jhazmat.2023.131243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/24/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
In situ bioremediation using organohalide-respiring bacteria (OHRB) is a prospective method for the removal of persistent halogenated organic pollutants from groundwater, as OHRB can utilize H2 or organic compounds produced by carbon source materials as electron donors for cell growth through organohalide respiration. However, few previous studies have determined the suitability of different carbon source materials to the metabolic mechanism of reductive dehalogenation from the perspective of electron transfer. The focus of this critical review was to reveal the interactions and relationships between carbon source materials and functional microbes, in terms of the electron transfer mechanism. Furthermore, this review illustrates some innovative strategies that have used the physiological characteristics of OHRB to guide the optimization of carbon source materials, improving the abundance of indigenous dehalogenated bacteria and enhancing electron transfer efficiency. Finally, it is proposed that future research should combine multi-omics analysis with machine learning (ML) to guide the design of effective carbon source materials and optimize current dehalogenation bioremediation strategies to reduce the cost and footprint of practical groundwater bioremediation applications.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yueyan Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yuqing Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Mengran Lv
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zeyi Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Li-Lian Wen
- College of Resource and Environmental Science, Hubei University, Wuhan 430062, China.
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Gao P, Fan K. Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in oil reservoir and biological control of SRB: a review. Arch Microbiol 2023; 205:162. [PMID: 37010699 DOI: 10.1007/s00203-023-03520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/18/2023] [Accepted: 03/26/2023] [Indexed: 04/04/2023]
Abstract
Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.
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Affiliation(s)
- Peike Gao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Keyan Fan
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
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7
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Willemin MS, Hamelin R, Armand F, Holliger C, Maillard J. Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms. Front Microbiol 2023; 14:1058127. [PMID: 36733918 PMCID: PMC9888536 DOI: 10.3389/fmicb.2023.1058127] [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: 09/30/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Introduction Desulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified. Methods In the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393. Results and discussion This dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium - a very widespread practice in the cultivation of strictly anaerobic bacteria - triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Hamelin
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Armand
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland,*Correspondence: Julien Maillard, ✉
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Cimmino L, Schmid AW, Holliger C, Maillard J. Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT. Front Microbiol 2022; 13:838026. [PMID: 35283847 PMCID: PMC8905343 DOI: 10.3389/fmicb.2022.838026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC, and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA2B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrien W Schmid
- Protein Core Facility, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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9
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Zhu X, Wang X, Li N, Wang Q, Liao C. Bioelectrochemical system for dehalogenation: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 293:118519. [PMID: 34793908 DOI: 10.1016/j.envpol.2021.118519] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/26/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Halogenated organic compounds are persistent pollutants, whose persistent contamination and rapid spread seriously threaten human health and the safety of ecosystems. It is difficult to remove them completely by traditional physicochemical techniques. In-situ remediation utilizing bioelectrochemical technology represents a promising strategy for degradation of halogenated organic compounds, which can be achieved through potential modulation. In this review, we summarize the reactor configuration of microbial electrochemical dehalogenation systems and relevant organohalide-respiring bacteria. We also highlight the mechanisms of electrode potential regulation of microbial dehalogenation and the role of extracellular electron transfer in dehalogenation process, and further discuss the application of bioelectrochemical technology in bioremediation of halogenated organic compounds. Therefore, this review summarizes the status of research on microbial electrochemical dehalogenation systems from macroscopic to microscopic levels, providing theoretical support for the development of rapid and efficient in situ bioremediation technologies for halogenated organic compounds contaminated sites, as well as insights for the removal of refractory fluorides.
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Affiliation(s)
- Xuemei Zhu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Qi Wang
- Beijing Construction Engineering Group Environmental Remediation Co. Ltd. and National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
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10
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Willemin MS, Vingerhoets M, Holliger C, Maillard J. Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria. Front Microbiol 2020; 11:310. [PMID: 32194528 PMCID: PMC7062800 DOI: 10.3389/fmicb.2020.00310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/12/2020] [Indexed: 11/13/2022] Open
Abstract
The bioremediation of persistent organohalide molecules under anoxic conditions mostly relies on the bacterial process called organohalide respiration (OHR). Organohalide-respiring bacteria (OHRB) are phylogenetically diverse anaerobic bacteria that share the capacity to use organohalides as terminal electron acceptors in an energy-conserving process. The reductive dehalogenase (rdh) gene clusters encode for proteins specialized in the respiration of one or a limited number of organohalides. One particular OHRB may harbor up to several dozens of rdh gene clusters suggesting a wide potential for bioremediation. To avoid wasting energy in producing unnecessary proteins, rdh gene clusters often include a transcriptional regulator. In organohalide-respiring Firmicutes, RdhK is a dedicated transcriptional regulator of OHR and represents a subfamily of proteins among the CRP/FNR superfamily of regulators. RdhK proteins are composed of an effector-binding domain (EBD) which recognizes a given organohalide and subsequently controls the interaction of its C-terminal DNA-binding domain (DBD) with a DNA motif (referred to as dehalobox, or DB) located in the promoter region of the target rdh genes. The two binding partners (i.e. an organohalide molecule and a DB sequence) of RdhK proteins are interdependent which impairs the exploration of OHR regulatory networks. Here, we propose a strategy relying on hybrid proteins to efficiently screen the DNA target of a single RdhK protein without prior knowledge on its effector. To demonstrate the potential of the method, two hybrids with alternative fusion points were designed based on RdhK6 EBD and RdhK1 DBD from Desulfitobacterium hafniense. Electrophoretic mobility shift assay was performed with purified hybrids along with the parental proteins and their binding properties were further tested in vivo through a β-galactosidase reporter assay. Along with revealing new RdhK6 features, we show that both hybrids resulted in active regulatory proteins with distinct binding patterns. While Hybrid A was less specific for the DNA motif, Hybrid B successfully mimicked the binding behavior of the parental proteins and thus represents a promising template for the design of new RdhK hybrids to screen yet uncharacterized RdhK proteins and also possibly other members of the CRP/FNR superfamily.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie Vingerhoets
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Liu J, Adrian L, Häggblom MM. Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor. Appl Environ Microbiol 2020; 86:e02146-19. [PMID: 31836581 PMCID: PMC7028966 DOI: 10.1128/aem.02146-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/10/2019] [Indexed: 01/31/2023] Open
Abstract
Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites.IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Fachgebiet Geobiotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
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12
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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13
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Abstract
Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. In this chapter, we present the major findings concerning the regulatory strategies developed by OHRB to control the expression of the rdh gene clusters. The first section focuses on the description of regulation patterns obtained from targeted transcriptional analyses, and from transcriptomic and proteomic studies, while the second section offers a detailed overview of the biochemically characterized OHR regulatory proteins identified so far. Depending on OHRB, transcriptional regulators belonging to three different protein families are found in the direct vicinity of rdh gene clusters, suggesting that they activate the transcription of their cognate gene cluster. In this chapter, strong emphasis was laid on the family of CRP/FNR-type RdhK regulators which belong to members of the genera Dehalobacter and Desulfitobacterium. Whereas only chlorophenols have been identified as effectors for RdhK regulators, the protein sequence diversity suggests a broader organohalide spectrum. Thus, effector identification of new regulators offers a promising alternative to elucidate the substrates of yet uncharacterized reductive dehalogenases. Future work investigating the possible cross-talk between OHR regulators and their possible use as biosensors is discussed.
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14
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Lechner U, Türkowsky D, Dinh TTH, Al‐Fathi H, Schwoch S, Franke S, Gerlach M, Koch M, von Bergen M, Jehmlich N, Dang TCH. Desulfitobacterium contributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill. Microb Biotechnol 2018; 11:1137-1156. [PMID: 30117290 PMCID: PMC6196390 DOI: 10.1111/1751-7915.13301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/07/2018] [Indexed: 12/17/2022] Open
Abstract
The herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) was a major component of Agent Orange, which was used as a defoliant in the Vietnam War. Little is known about its degradation under anoxic conditions. Established enrichment cultures using soil from an Agent Orange bioremediation plant in southern Vietnam with pyruvate as potential electron donor and carbon source were shown to degrade 2,4,5-T via ether cleavage to 2,4,5-trichlorophenol (2,4,5-TCP), which was further dechlorinated to 3,4-dichlorophenol. Pyruvate was initially fermented to hydrogen, acetate and propionate. Hydrogen was then used as the direct electron donor for ether cleavage of 2,4,5-T and subsequent dechlorination of 2,4,5-TCP. 16S rRNA gene amplicon sequencing indicated the presence of bacteria and archaea mainly belonging to the Firmicutes, Bacteroidetes, Spirochaetes, Chloroflexi and Euryarchaeota. Desulfitobacterium hafniense was identified as the dechlorinating bacterium. Metaproteomics of the enrichment culture indicated higher protein abundances of 60 protein groups in the presence of 2,4,5-T. A reductive dehalogenase related to RdhA3 of D. hafniense showed the highest fold change, supporting its function in reductive dehalogenation of 2,4,5-TCP. Despite an ether-cleaving enzyme not being detected, the inhibition of ether cleavage but not of dechlorination, by 2-bromoethane sulphonate, suggested that the two reactions are catalysed by different organisms.
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Affiliation(s)
- Ute Lechner
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Dominique Türkowsky
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Thi Thu Hang Dinh
- Vietnamese Academy of Science and TechnologyInstitute of BiotechnologyHanoiVietnam
- Present address:
Vietnamese Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Hassan Al‐Fathi
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Stefan Schwoch
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Stefan Franke
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | | | - Mandy Koch
- Institute of Chemistry/Food and Environmental ChemistryMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Martin von Bergen
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Thi Cam Ha Dang
- Vietnamese Academy of Science and TechnologyInstitute of BiotechnologyHanoiVietnam
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15
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Wang S, Qiu L, Liu X, Xu G, Siegert M, Lu Q, Juneau P, Yu L, Liang D, He Z, Qiu R. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol Adv 2018; 36:1194-1206. [DOI: 10.1016/j.biotechadv.2018.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/08/2023]
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16
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Marozava S, Vargas-López R, Tian Y, Merl-Pham J, Braster M, Meckenstock RU, Smidt H, Röling WFM, Westerhoff HV. Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats. Environ Microbiol 2018; 20:2652-2669. [PMID: 29921035 DOI: 10.1111/1462-2920.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 05/19/2018] [Indexed: 11/30/2022]
Abstract
Desulfitobacterium hafniense Y51 has been widely used in investigations of perchloroethylene (PCE) biodegradation, but limited information exists on its other physiological capabilities. We investigated how D. hafniense Y51 confronts the debilitating limitations of not having enough electron donor (lactate), or electron acceptor (fumarate) during cultivation in chemostats. The residual concentrations of the substrates supplied in excess were much lower than expected. Transcriptomics, proteomics and fluxomics were integrated to investigate how this phenomenon was regulated. Through diverse regulation at both transcriptional and translational levels, strain Y51 turned to fermenting the excess lactate and disproportionating the excess fumarate under fumarate- and lactate-limiting conditions respectively. Genes and proteins related to the utilization of a variety of alternative electron donors and acceptors absent from the medium were induced, apparently involving the Wood-Ljungdahl pathway. Through this metabolic flexibility, D. hafniense Y51 may be able to switch between different metabolic capabilities under limiting conditions.
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Affiliation(s)
- Sviatlana Marozava
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Raquel Vargas-López
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Ye Tian
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Juliane Merl-Pham
- Core Facility Proteomics, Helmholtz Zentrum München, Heidemannstraße 1, 80939, München, Germany
| | - Martin Braster
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Rainer U Meckenstock
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Wilfred F M Röling
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Hans V Westerhoff
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands.,Synthetic Systems Biology, SILS, University of Amsterdam, Amsterdam, The Netherlands.,Manchester Centre for Integrative Systems Biology, School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, UK
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17
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Buttet GF, Willemin MS, Hamelin R, Rupakula A, Maillard J. The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC. Front Microbiol 2018; 9:755. [PMID: 29740408 PMCID: PMC5928378 DOI: 10.3389/fmicb.2018.00755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/04/2018] [Indexed: 12/15/2022] Open
Abstract
Organohalide respiration (OHR) is the energy metabolism of anaerobic bacteria able to use halogenated organic compounds as terminal electron acceptors. While the terminal enzymes in OHR, so-called reductive dehalogenases, are well-characterized, the identity of proteins potentially involved in electron transfer to the terminal enzymes remains elusive. Among the accessory genes identified in OHR gene clusters, the C subunit (rdhC) could well code for the missing redox protein between the quinol pool and the reductive dehalogenase, although it was initially proposed to act as transcriptional regulator. RdhC sequences are characterized by the presence of multiple transmembrane segments, a flavin mononucleotide (FMN) binding motif and two conserved CX3CP motifs. Based on these features, we propose a curated selection of RdhC proteins identified in general sequence databases. Beside the Firmicutes from which RdhC sequences were initially identified, the identified sequences belong to three additional phyla, the Chloroflexi, the Proteobacteria, and the Bacteriodetes. The diversity of RdhC sequences mostly respects the phylogenetic distribution, suggesting that rdhC genes emerged relatively early in the evolution of the OHR metabolism. PceC, the C subunit of the tetrachloroethene (PCE) reductive dehalogenase is encoded by the conserved pceABCT gene cluster identified in Dehalobacter restrictus PER-K23 and in several strains of Desulfitobacterium hafniense. Surfaceome analysis of D. restrictus cells confirmed the predicted topology of the FMN-binding domain (FBD) of PceC that is the exocytoplasmic face of the membrane. Starting from inclusion bodies of a recombinant FBD protein, strategies for successful assembly of the FMN cofactor and refolding were achieved with the use of the flavin-trafficking protein from D. hafniense TCE1. Mass spectrometry analysis and site-directed mutagenesis of rFBD revealed that threonine-168 of PceC is binding FMN covalently. Our results suggest that PceC, and more generally RdhC proteins, may play a role in electron transfer in the metabolism of OHR.
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Affiliation(s)
- Géraldine F Buttet
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Mathilde S Willemin
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Romain Hamelin
- Protein Core Facility, Faculty of Life Sciences, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Aamani Rupakula
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
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18
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Schubert T, Adrian L, Sawers RG, Diekert G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol Ecol 2018; 94:4923014. [DOI: 10.1093/femsec/fiy035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
- Department of Geobiotechnology, Technische Universität Berlin, Ackerstraße 74, D-13355 Berlin, Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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19
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Kruse T, Goris T, Maillard J, Woyke T, Lechner U, de Vos W, Smidt H. Comparative genomics of the genus Desulfitobacterium. FEMS Microbiol Ecol 2017; 93:4443196. [DOI: 10.1093/femsec/fix135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/10/2017] [Indexed: 02/03/2023] Open
Affiliation(s)
- Thomas Kruse
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, ENAC-IIE-LBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Ute Lechner
- Institute of Biology/Microbiology, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle 06120, Germany
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Helsinki University, P.O. Box 21, 00014 Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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20
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Affiliation(s)
- Maeva Fincker
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
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21
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Schubert T. The organohalide-respiring bacterium Sulfurospirillum multivorans: a natural source for unusual cobamides. World J Microbiol Biotechnol 2017; 33:93. [DOI: 10.1007/s11274-017-2258-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/01/2017] [Indexed: 01/27/2023]
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22
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Kruse S, Goris T, Wolf M, Wei X, Diekert G. The NiFe Hydrogenases of the Tetrachloroethene-Respiring Epsilonproteobacterium Sulfurospirillum multivorans: Biochemical Studies and Transcription Analysis. Front Microbiol 2017; 8:444. [PMID: 28373866 PMCID: PMC5357620 DOI: 10.3389/fmicb.2017.00444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/03/2017] [Indexed: 12/24/2022] Open
Abstract
The organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans is able to grow with hydrogen as electron donor and with tetrachloroethene (PCE) as electron acceptor; PCE is reductively dechlorinated to cis-1,2-dichloroethene. Recently, a genomic survey revealed the presence of four gene clusters encoding NiFe hydrogenases in its genome, one of which is presumably periplasmic and membrane-bound (MBH), whereas the remaining three are cytoplasmic. To explore the role and regulation of the four hydrogenases, quantitative real-time PCR and biochemical studies were performed with S. multivorans cells grown under different growth conditions. The large subunit genes of the MBH and of a cytoplasmic group 4 hydrogenase, which is assumed to be membrane-associated, show high transcript levels under nearly all growth conditions tested, pointing toward a constitutive expression in S. multivorans. The gene transcripts encoding the large subunits of the other two hydrogenases were either not detected at all or only present at very low amounts. The presence of MBH under all growth conditions tested, even with oxygen as electron acceptor under microoxic conditions, indicates that MBH gene transcription is not regulated in contrast to other facultative hydrogen-oxidizing bacteria. The MBH showed quinone-reactivity and a characteristic UV/VIS spectrum implying a cytochrome b as membrane-integral subunit. Cell extracts of S. multivorans were subjected to native polyacrylamide gel electrophoresis (PAGE) and hydrogen oxidizing activity was tested by native staining. Only one band was detected at about 270 kDa in the particulate fraction of the extracts, indicating that there is only one hydrogen-oxidizing enzyme present in S. multivorans. An enrichment of this enzyme and SDS PAGE revealed a subunit composition corresponding to that of the MBH. From these findings we conclude that the MBH is the electron-donating enzyme system in the PCE respiratory chain. The roles for the other three hydrogenases remain unproven. The group 4 hydrogenase might be involved in hydrogen production upon fermentative growth.
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Affiliation(s)
- Stefan Kruse
- Department of Applied and Ecological Microbiology, Institute of Microbiology Friedrich Schiller University, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology Friedrich Schiller University, Germany
| | - Maria Wolf
- Department of Applied and Ecological Microbiology, Institute of Microbiology Friedrich Schiller University, Germany; Dianovis GmbHGreiz, Germany
| | - Xi Wei
- Department of Applied and Ecological Microbiology, Institute of Microbiology Friedrich Schiller University, Germany; Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZLeipzig, Germany; YMC Europe GmbHDinslaken, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology Friedrich Schiller University, Germany
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23
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Jugder BE, Ertan H, Wong YK, Braidy N, Manefield M, Marquis CP, Lee M. Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:814-824. [PMID: 27452500 DOI: 10.1111/1758-2229.12444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Organohalide respiring bacteria (ORB) are capable of utilising organohalides as electron acceptors for the generation of cellular energy and consequently play an important role in the turnover of natural and anthropogenically-derived organohalides. In this study, the response of a Dehalobacter sp. strain UNSWDHB to the addition of trichloromethane (TCM) after a 50 h period of its absence (suffocation) was evaluated from a transcriptomic and proteomic perspective. The up-regulation of TCM reductive dehalogenase genes (tmrABC) and their gene products (TmrABC) was confirmed at both transcriptional and proteomic levels. Other findings include the upregulation of various hydrogenases (membrane-associated Ni-Fe hydrogenase complexes and soluble Fe-Fe hydrogenases), formate dehydrogenases, complex I and a pyrophosphate-energized proton pump. The elevated expression of enzymes associated with carbon metabolism, including complete Wood Ljungdahl pathway, during TCM respiration raises interesting questions on possible fates of intracellular formate and its potential role in the physiology of this bacterium. Overall, the findings presented here provide a broader view on the bioenergetics and general physiology of Dehalobacter UNSWDHB cells actively respiring with TCM.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
- Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Yie Kuan Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Nady Braidy
- Faculty of Medicine, School of Psychiatry, Centre for Healthy Brain Ageing, University of New South Wales, Sydney, Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
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24
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Jugder BE, Ertan H, Bohl S, Lee M, Marquis CP, Manefield M. Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation. Front Microbiol 2016; 7:249. [PMID: 26973626 PMCID: PMC4771760 DOI: 10.3389/fmicb.2016.00249] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 01/31/2023] Open
Abstract
Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia; Department of Molecular Biology and Genetics, Istanbul UniversityIstanbul, Turkey
| | - Susanne Bohl
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia; Department of Biotechnology, Mannheim University of Applied SciencesMannheim, Germany
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
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25
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Kublik A, Deobald D, Hartwig S, Schiffmann CL, Andrades A, von Bergen M, Sawers RG, Adrian L. Identification of a multi-protein reductive dehalogenase complex inDehalococcoides mccartyistrain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement. Environ Microbiol 2016; 18:3044-56. [DOI: 10.1111/1462-2920.13200] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/03/2015] [Accepted: 12/23/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Anja Kublik
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Darja Deobald
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Stefanie Hartwig
- Institute of Microbiology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle Germany
| | - Christian L. Schiffmann
- Department of Proteomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Adarelys Andrades
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Proteomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
- Department of Metabolomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
- Centre for Microbial Communities; University of Aalborg; Fredrik Bajers Vej 7H 9220 Aalborg East Denmark
| | - R. Gary Sawers
- Institute of Microbiology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
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Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates. Sci Rep 2015; 5:13794. [PMID: 26387727 PMCID: PMC4585668 DOI: 10.1038/srep13794] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 08/05/2015] [Indexed: 12/15/2022] Open
Abstract
Organohalide respiration is an environmentally important but poorly characterized type of anaerobic respiration. We compared the global proteome of the versatile organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans grown with different electron acceptors (fumarate, nitrate, or tetrachloroethene [PCE]). The most significant differences in protein abundance were found for gene products of the organohalide respiration region. This genomic region encodes the corrinoid and FeS cluster containing PCE reductive dehalogenase PceA and other proteins putatively involved in PCE metabolism such as those involved in corrinoid biosynthesis. The latter gene products as well as PceA and a putative quinol dehydrogenase were almost exclusively detected in cells grown with PCE. This finding suggests an electron flow from the electron donor such as formate or pyruvate via the quinone pool and a quinol dehydrogenase to PceA and the terminal electron acceptor PCE. Two putative accessory proteins, an IscU-like protein and a peroxidase-like protein, were detected with PCE only and might be involved in PceA maturation. The proteome of cells grown with pyruvate instead of formate as electron donor indicates a route of electrons from reduced ferredoxin via an Epsilonproteobacterial complex I and the quinone pool to PCE.
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