1
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Thulluru LP, Ghangrekar MM, Chowdhury S. Progress and perspectives on microbial electrosynthesis for valorisation of CO 2 into value-added products. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117323. [PMID: 36716542 DOI: 10.1016/j.jenvman.2023.117323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/06/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Microbial electrosynthesis (MES) is a neoteric technology that facilitates biocatalysed synthesis of organic compounds with the aid of homoacetogenic bacteria, while feeding CO2 as an inorganic carbon source. Operating MES with surplus renewable electricity further enhances the sustainability of this innovative bioelectrochemical system (BES). However, several lacunae exist in the domain knowledge, stunting the widespread application of MES. Despite significant progress in this area over the past decade, the product yield efficiency is not on par with other contemporary technologies. This bottleneck can be overcome by adopting a holistic approach, i.e., applying innovative and integrated solutions to ensure a robust MES operation. Further, the widespread deployment of MES exclusively relies on its ability to mature a sessile biofilm over a biocompatible electrode, while offering minimal charge transfer resistance. Additionally, operating MES preferably at H2-generating reduction potential and valorising industrial off-gas as carbon substrate is crucial to accomplish economic sustainability. In light of the aforementioned, this review collates the latest progress in the design and development of MES-centred systems for valorisation of CO2 into value-added products. Specifically, it highlights the significance of inoculum pre-treatment for promoting biocatalytic activity and biofilm growth on the cathodic surface. In addition, it summarizes the diverse materials that are commonly used as electrodes in MES, with an emphasis on the importance of inexpensive, robust, and biocompatible electrode materials for the practical application of MES technology. Further, the review presents insights into media conditions, operational factors, and reactor configurations that affect the overall performance of MES process. Finally, the product range of MES, downstream processing requirements, and integration of MES with other environmental remediation technologies are also discussed.
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Affiliation(s)
- Lakshmi Pathi Thulluru
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Makarand M Ghangrekar
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Shamik Chowdhury
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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2
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Zhao Z, Zheng D, Guo M, Yu J, Zhang S, Zhang Z, Chen Y. Engineering Olefin-Linked Covalent Organic Frameworks for Photoenzymatic Reduction of CO 2. Angew Chem Int Ed Engl 2022; 61:e202200261. [PMID: 35041240 DOI: 10.1002/anie.202200261] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Indexed: 12/20/2022]
Abstract
It is of profound significance concerning the global energy and environmental crisis to develop new techniques that can reduce and convert CO2 . To address this challenge, we built a new type of artificial photoenzymatic system for CO2 reduction, using a rationally designed mesoporous olefin-linked covalent organic framework (COF) as the porous solid carrier for co-immobilizing formate dehydrogenase (FDH) and Rh-based electron mediator. By adjusting the incorporating content of the Rh electronic mediator, which facilitates the regeneration of nicotinamide cofactor (NADH) from NAD+ , the apparent quantum yield can reach as high as 9.17±0.44 %, surpassing all reported NADH-regenerated photocatalysts constructed by crystalline framework materials. Finally, the assembled photocatalyst-enzyme coupled system can selectively convert CO2 to formic acid with high efficiency and good reusability. This work demonstrates the first example using COFs to immobilize enzymes for artificial photosynthesis systems that utilize solar energy to produce value-added chemicals.
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Affiliation(s)
- Zhengfeng Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China.,School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Dong Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Menglei Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jiangyue Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Sainan Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Zhenjie Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Key Laboratory of Advanced Energy Materials Chemistry, Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yao Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
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3
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Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism. Catalysts 2022. [DOI: 10.3390/catal12020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.
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4
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Zhao Z, Zheng D, Guo M, Yu J, Zhang S, Zhang Z, Chen Y. Engineering Olefin‐Linked Covalent Organic Frameworks for Photoenzymatic Reduction of CO2. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Dong Zheng
- Nankai University College of Pharmacy CHINA
| | | | | | | | | | - Yao Chen
- Nankai University State Key Laboratory of Medicinal Chemical Biology, Nankai University Weijin Road 94# Tianjin CHINA
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5
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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6
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Screening of Gas Substrate and Medium Effects on 2,3-Butanediol Production with C. ljungdahlii and C. autoethanogenum Aided by Improved Autotrophic Cultivation Technique. FERMENTATION 2021. [DOI: 10.3390/fermentation7040264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gas fermentation by acetogens of the genus Clostridium is an attractive technology since it affords the production of biochemicals and biofuels from industrial waste gases while contributing to mitigate the carbon cycle alterations. The acetogenic model organisms C. ljungdahlii and C. autoethanogenum have already been used in large scale industrial fermentations. Among the natural products, ethanol production has already attained industrial scale. However, some acetogens are also natural producers of 2,3-butanediol (2,3-BDO), a platform chemical of relevant industrial interest. Here, we have developed a lab-scale screening campaign with the aim of enhancing 2,3-BDO production. Our study generated comparable data on growth and 2,3-BDO production of several batch gas fermentations using C. ljungdahlii and C. autoethanogenum grown on different gas substrates of primary applicative interest (CO2 · H2, CO · CO2, syngas) and on different media featuring different compositions as regards trace metals, mineral elements and vitamins. CO · CO2 fermentation was found to be preferable for the production of 2,3-BDO, and a fair comparison of the strains cultivated in comparable conditions revealed that C. ljungdahlii produced 3.43-fold higher titer of 2,3-BDO compared to C. autoethanogenum. Screening of different medium compositions revealed that mineral elements, Zinc and Iron exert a major positive influence on 2,3-BDO titer and productivity. Moreover, the CO2 influence on CO fermentation was explored by characterizing C. ljungdahlii response with respect to different gas ratios in the CO · CO2 gas mixtures. The screening strategies undertaken in this study led to the production of 2.03 ± 0.05 g/L of 2,3-BDO, which is unprecedented in serum bottle experiments.
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7
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Fackler N, Heijstra BD, Rasor BJ, Brown H, Martin J, Ni Z, Shebek KM, Rosin RR, Simpson SD, Tyo KE, Giannone RJ, Hettich RL, Tschaplinski TJ, Leang C, Brown SD, Jewett MC, Köpke M. Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation. Annu Rev Chem Biomol Eng 2021; 12:439-470. [PMID: 33872517 DOI: 10.1146/annurev-chembioeng-120120-021122] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.
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Affiliation(s)
- Nick Fackler
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | | | - Blake J Rasor
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Hunter Brown
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Jacob Martin
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Zhuofu Ni
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Kevin M Shebek
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Rick R Rosin
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Séan D Simpson
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Keith E Tyo
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | | | - Ching Leang
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Steven D Brown
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , , .,Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, USA
| | - Michael Köpke
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
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8
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Han YF, Xie BT, Wu GX, Guo YQ, Li DM, Huang ZY. Combination of Trace Metal to Improve Solventogenesis of Clostridium carboxidivorans P7 in Syngas Fermentation. Front Microbiol 2020; 11:577266. [PMID: 33101253 PMCID: PMC7546793 DOI: 10.3389/fmicb.2020.577266] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 11/13/2022] Open
Abstract
Higher alcohols such as butanol (C4 alcohol) and hexanol (C6 alcohol) are superior biofuels compared to ethanol. Clostridium carboxidivorans P7 is a typical acetogen capable of producing C4 and C6 alcohols natively. In this study, the composition of trace metals in culture medium was adjusted, and the effects of these adjustments on artificial syngas fermentation by C. carboxidivorans P7 were investigated. Nickel and ferrous ions were essential for growth and metabolite synthesis during syngas fermentation by P7. However, a decreased dose of molybdate improved alcohol fermentation performance by stimulating carbon fixation and solventogenesis. In response to the modified trace metal composition, cells grew to a maximum OD600 nm of 1.6 and accumulated ethanol and butanol to maximum concentrations of 2.0 and 1.0 g/L, respectively, in serum bottles. These yields were ten-fold higher than the yields generated using the original composition of trace metals. Furthermore, 0.5 g/L of hexanol was detected at the end of fermentation. The results from gene expression experiments examining genes related to carbon fixation and organic acid and solvent synthesis pathways revealed a dramatic up-regulation of the Wood-Ljungdahl pathway (WLP) gene cluster, the bcs gene cluster, and a putative CoA transferase and butanol dehydrogenase, thereby indicating that both de novo synthesis and acid re-assimilation contributed to the significantly elevated accumulation of higher alcohols. The bdh35 gene was speculated to be the key target for butanol synthesis during solventogenesis.
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Affiliation(s)
- Yi-Fan Han
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Bin-Tao Xie
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Guang-Xun Wu
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ya-Qiong Guo
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - De-Mao Li
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhi-Yong Huang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
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9
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Affiliation(s)
- Cláudio J. R. Frazão
- TU Dresden Institute of Natural Materials Technology Bergstraße 120 01062 Dresden Germany
| | - Thomas Walther
- TU Dresden Institute of Natural Materials Technology Bergstraße 120 01062 Dresden Germany
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10
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Kang S, Song Y, Jin S, Shin J, Bae J, Kim DR, Lee JK, Kim SC, Cho S, Cho BK. Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide. Front Microbiol 2020; 11:402. [PMID: 32218779 PMCID: PMC7079680 DOI: 10.3389/fmicb.2020.00402] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/26/2020] [Indexed: 11/13/2022] Open
Abstract
Acetogens are naturally capable of metabolizing carbon monoxide (CO), a component of synthesis gas (syngas), for autotrophic growth in order to produce biomass and metabolites such as acetyl-CoA via the Wood–Ljungdahl pathway. However, the autotrophic growth of acetogens is often inhibited by the presence of high CO concentrations because of CO toxicity, thus limiting their biosynthetic potential for industrial applications. Herein, we implemented adaptive laboratory evolution (ALE) for growth improvement of Eubacterium limosum ATCC 8486 under high CO conditions. The strain evolved under syngas conditions with 44% CO over 150 generations, resulting in a significant increased optical density (600 nm) and growth rate by 2.14 and 1.44 folds, respectively. In addition, the evolved populations were capable of proliferating under CO concentrations as high as 80%. These results suggest that cell growth is enhanced as beneficial mutations are selected and accumulated, and the metabolism is altered to facilitate the enhanced phenotype. To identify the causal mutations related to growth improvement under high CO concentrations, we performed whole genome resequencing of each population at 50-generation intervals. Interestingly, we found key mutations in CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex coding genes, acsA and cooC. To characterize the mutational effects on growth under CO, we isolated single clones and confirmed that the growth rate and CO tolerance level of the single clone were comparable to those of the evolved populations and wild type strain under CO conditions. Furthermore, the evolved strain produced 1.34 folds target metabolite acetoin when compared to the parental strain while introducing the biosynthetic pathway coding genes to the strains. Consequently, this study demonstrates that the mutations in the CODH/ACS complex affect autotrophic growth enhancement in the presence of CO as well as the CO tolerance of E. limosum ATCC 8486.
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Affiliation(s)
- Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Dong Rip Kim
- Department of Mechanical Engineering, Hanyang University, Seoul, South Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, South Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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11
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Wang SC. Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis. Nat Prod Rep 2019; 35:707-720. [PMID: 30079906 DOI: 10.1039/c7np00059f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.
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Affiliation(s)
- Susan C Wang
- Case Western Reserve University School of Medicine, Department of Biochemistry, USA.
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12
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Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS Comput Biol 2019; 15:e1006848. [PMID: 30845144 PMCID: PMC6430413 DOI: 10.1371/journal.pcbi.1006848] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 03/22/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens. Acetogens are renowned for their potential biotechnological applications. The model acetogen Clostridium ljungdahlii has been studied intensively for its ability to produce biofuels from sustainable resources, like syngas. We describe a novel genome-scale model of metabolism and gene expression (ME-model) to gain insights into this model acetogen. This first ME-model for a Gram-positive bacterium contains all major metabolic and biosynthetic pathways and calculates accurate proteome allocations under diverse growth conditions, thereby significantly broadening the scope of predictability of metabolic models. Furthermore, the ME-model enables rational medium design for improved production. Our experimental validation implies wide applicability to others strains for rapid improvement of yield and titer in biotechnology-relevant applications.
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Affiliation(s)
- Joanne K. Liu
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Colton Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Mahmoud M. Al-Bassam
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Ali Ebrahim
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Ji-Nu Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Connor Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Alexander Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, United States of America
| | - Pieter Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, United States of America
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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13
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Lapointe S, Khaskin E, Fayzullin RR, Khusnutdinova JR. Stable Nickel(I) Complexes with Electron-Rich, Sterically-Hindered, Innocent PNP Pincer Ligands. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sébastien Lapointe
- Okinawa Institute of Science and Technology Graduate University, Coordination Chemistry and Catalysis Unit, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Eugene Khaskin
- Okinawa Institute of Science and Technology Graduate University, Coordination Chemistry and Catalysis Unit, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FCR Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Julia R. Khusnutdinova
- Okinawa Institute of Science and Technology Graduate University, Coordination Chemistry and Catalysis Unit, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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14
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Manesis AC, Musselman BW, Keegan BC, Shearer J, Lehnert N, Shafaat HS. A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase. Inorg Chem 2019; 58:8969-8982. [PMID: 30788970 PMCID: PMC6635881 DOI: 10.1021/acs.inorgchem.8b03546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Nickel-containing
enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide
dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical
role in global energy conversion reactions, with significant contributions
to carbon-centered processes. These enzymes are implied to cycle through
a series of nickel-based organometallic intermediates during catalysis,
though identification of these intermediates remains challenging.
In this work, we have developed and characterized a nickel-containing
metalloprotein that models the methyl-bound organometallic intermediates
proposed in the native enzymes. Using a nickel(I)-substituted azurin
mutant, we demonstrate that alkyl binding occurs via nucleophilic
addition of methyl iodide as a methyl donor. The paramagnetic NiIII-CH3 species initially generated can be rapidly
reduced to a high-spin NiII-CH3 species in the
presence of exogenous reducing agent, following a reaction sequence
analogous to that proposed for ACS. These two distinct bioorganometallic
species have been characterized by optical, EPR, XAS, and MCD spectroscopy,
and the overall mechanism describing methyl reactivity with nickel
azurin has been quantitatively modeled using global kinetic simulations.
A comparison between the nickel azurin protein system and existing
ACS model compounds is presented. NiIII-CH3 Az
is only the second example of two-electron addition of methyl iodide
to a NiI center to give an isolable species and the first
to be formed in a biologically relevant system. These results highlight
the divergent reactivity of nickel across the two intermediates, with
implications for likely reaction mechanisms and catalytically relevant
states in the native ACS enzyme. A bioorganometallic model
for acetyl coenzyme A synthase has been developed. This model protein
is able to bind a cationic methyl group via direct addition to the
nickel(I) center. The resultant nickel(III)-methyl species has been
characterized via optical and electron paramagnetic resonance spectroscopy,
and the reduced nickel(II)-methyl state has been characterized using
magnetic circular dichroism and X-ray spectroscopy. Implications for
further reactivity with CO are gleaned from electronic structure analysis
of the nickel-methyl species.
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Affiliation(s)
- Anastasia C Manesis
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
| | - Bradley W Musselman
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brenna C Keegan
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Jason Shearer
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Nicolai Lehnert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
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15
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Xavier JC, Preiner M, Martin WF. Something special about CO-dependent CO 2 fixation. FEBS J 2018; 285:4181-4195. [PMID: 30240136 PMCID: PMC6282760 DOI: 10.1111/febs.14664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/08/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023]
Abstract
Carbon dioxide enters metabolism via six known CO2 fixation pathways, of which only one is linear, exergonic in the direction of CO2‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO2. We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO2, which are non‐randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO2, only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni‐ and Fe‐containing enzyme that generates CO for CO2 fixation in the WL pathway, and aerobic CODH, a Mo‐ and Cu‐containing enzyme that oxidizes environmental CO as an electron source. The CO‐dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon‐nickel at the Ni‐Fe‐S A‐cluster of acetyl‐CoA synthase (ACS). It appears that no alternative mechanisms to the CO‐dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.
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Affiliation(s)
- Joana C Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - Martina Preiner
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - William F Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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16
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Abdel Azim A, Rittmann SKMR, Fino D, Bochmann G. The physiological effect of heavy metals and volatile fatty acids on Methanococcus maripaludis S2. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:301. [PMID: 30410576 PMCID: PMC6214177 DOI: 10.1186/s13068-018-1302-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/25/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Methanogenic archaea are of importance to the global C-cycle and to biological methane (CH4) production through anaerobic digestion and pure culture. Here, the individual and combined effects of copper (Cu), zinc (Zn), acetate, and propionate on the metabolism of the autotrophic, hydrogenotrophic methanogen Methanococcus maripaludis S2 were investigated. Cu, Zn, acetate, and propionate may interfere directly and indirectly with the acetyl-CoA synthesis and biological CH4 production. Thus, these compounds can compromise or improve the performance of M. maripaludis, an organism which can be applied as biocatalyst in the carbon dioxide (CO2)-based biological CH4 production (CO2-BMP) process or of methanogenic organisms applied in anaerobic digestion. RESULTS Here, we show that Cu concentration of 1.9 µmol L-1 reduced growth of M. maripaludis, whereas 4.4 and 6.3 µmol L-1 of Cu even further retarded biomass production. However, 1.0 mmol L-1 of Zn enhanced growth, but at Zn concentrations > 2.4 mmol L-1 no growth could be observed. When both, Cu and Zn, were supplemented to the medium, growth and CH4 production could even be observed at the highest tested concentration of Cu (6.3 µmol L-1). Hence, it seems that the addition of 1 mmol L-1 of Zn enhanced the ability of M. maripaludis to counteract the toxic effect of Cu. The physiological effect to rising concentrations of acetate (12.2, 60.9, 121.9 mmol L-1) and/or propionate (10.3, 52.0, 104.1 mmol L-1) was also investigated. When instead of acetate 10.3 mmol L-1 propionate was provided in the growth medium, M. maripaludis could grow without reduction of the specific growth rate (µ) or the specific CH4 productivity (qCH4). A combination of inorganic and/or organic compounds resulted in an increase of µ and qCH4 for Zn/Cu and Zn/acetate beyond the values that were observed if only the individual concentrations of Zn, Cu, acetate were used. CONCLUSIONS Our study sheds light on the physiological effect of VFAs and heavy metals on M. maripaludis. Differently from µ and qCH4, MER was not influenced by the presence of these compounds. This indicated that each of these compounds directly interacted with the C-fixation machinery of M. maripaludis. Until now, the uptake of VFAs other than acetate was not considered to enhance growth and CH4 production of methanogens. The finding of propionate uptake by M. maripaludis is important for the interpretation of VFA cycling in anaerobic microenvironments. Due to the importance of methanogens in natural and artificial anaerobic environments, our results help to enhance the understanding the physiological and biotechnological importance with respect to anaerobic digestion, anaerobic wastewater treatment, and CO2-BMP. Finally, we propose a possible mechanism for acetate uptake into M. maripaludis supported by in silico analyses.
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Affiliation(s)
- Annalisa Abdel Azim
- Institute for Environmental Biotechnology, IFA Department Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090 Vienna, Austria
- Department of Applied Science and Technology (DISAT), Politecnico di Torino, Turin, Italy
- Center for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Turin, Italy
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090 Vienna, Austria
| | - Debora Fino
- Department of Applied Science and Technology (DISAT), Politecnico di Torino, Turin, Italy
| | - Günther Bochmann
- Institute for Environmental Biotechnology, IFA Department Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
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17
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Heterologous Expression of the Clostridium carboxidivorans CO Dehydrogenase Alone or Together with the Acetyl Coenzyme A Synthase Enables both Reduction of CO 2 and Oxidation of CO by Clostridium acetobutylicum. Appl Environ Microbiol 2017. [PMID: 28625981 DOI: 10.1128/aem.00829-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
With recent advances in synthetic biology, CO2 could be utilized as a carbon feedstock by native or engineered organisms, assuming the availability of electrons. Two key enzymes used in autotrophic CO2 fixation are the CO dehydrogenase (CODH) and acetyl coenzyme A (acetyl-CoA) synthase (ACS), which form a bifunctional heterotetrameric complex. The CODH/ACS complex can reversibly catalyze CO2 to CO, effectively enabling a biological water-gas shift reaction at ambient temperatures and pressures. The CODH/ACS complex is part of the Wood-Ljungdahl pathway (WLP) used by acetogens to fix CO2, and it has been well characterized in native hosts. So far, only a few recombinant CODH/ACS complexes have been expressed in heterologous hosts, none of which demonstrated in vivo CO2 reduction. Here, functional expression of the Clostridium carboxidivorans CODH/ACS complex is demonstrated in the solventogen Clostridium acetobutylicum, which was engineered to express CODH alone or together with the ACS. Both strains exhibited CO2 reduction and CO oxidation activities. The CODH reactions were interrogated using isotopic labeling, thus verifying that CO was a direct product of CO2 reduction, and vice versa. CODH apparently uses a native C. acetobutylicum ferredoxin as an electron carrier for CO2 reduction. Heterologous CODH activity depended on actively growing cells and required the addition of nickel, which is inserted into CODH without the need to express the native Ni insertase protein. Increasing CO concentrations in the gas phase inhibited CODH activity and altered the metabolite profile of the CODH-expressing cells. This work provides the foundation for engineering a complete and functional WLP in nonnative host organisms.IMPORTANCE Functional expression of CO dehydrogenase (CODH) from Clostridium carboxidivorans was demonstrated in C. acetobutylicum, which is natively incapable of CO2 fixation. The expression of CODH, alone or together with the C. carboxidivorans acetyl-CoA synthase (ACS), enabled C. acetobutylicum to catalyze both CO2 reduction and CO oxidation. Importantly, CODH exhibited activity in both the presence and absence of ACS. 13C-tracer studies confirmed that the engineered C. acetobutylicum strains can reduce CO2 to CO and oxidize CO during growth on glucose.
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18
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Manesis AC, O'Connor MJ, Schneider CR, Shafaat HS. Multielectron Chemistry within a Model Nickel Metalloprotein: Mechanistic Implications for Acetyl-CoA Synthase. J Am Chem Soc 2017; 139:10328-10338. [PMID: 28675928 DOI: 10.1021/jacs.7b03892] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The acetyl coenzyme A synthase (ACS) enzyme plays a central role in the metabolism of anaerobic bacteria and archaea, catalyzing the reversible synthesis of acetyl-CoA from CO and a methyl group through a series of nickel-based organometallic intermediates. Owing to the extreme complexity of the native enzyme systems, the mechanism by which this catalysis occurs remains poorly understood. In this work, we have developed a protein-based model for the NiP center of acetyl coenzyme A synthase using a nickel-substituted azurin protein (NiAz). NiAz is the first model nickel protein system capable of accessing three (NiI/NiII/NiIII) distinct oxidation states within a physiological potential range in aqueous solution, a critical feature for achieving organometallic ACS activity, and binds CO and -CH3 groups with biologically relevant affinity. Characterization of the NiI-CO species through spectroscopic and computational techniques reveals fundamentally similar features between the model NiAz system and the native ACS enzyme, highlighting the potential for related reactivity in this model protein. This work provides insight into the enzymatic process, with implications toward engineering biological catalysts for organometallic processes.
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Affiliation(s)
- Anastasia C Manesis
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Matthew J O'Connor
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Camille R Schneider
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
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19
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De Tissera S, Köpke M, Simpson SD, Humphreys C, Minton NP, Dürre P. Syngas Biorefinery and Syngas Utilization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017. [DOI: 10.1007/10_2017_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Quantum chemical approaches to [NiFe] hydrogenase. Essays Biochem 2017; 61:293-303. [PMID: 28487405 DOI: 10.1042/ebc20160079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.
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21
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Schrapers P, Ilina J, Gregg CM, Mebs S, Jeoung JH, Dau H, Dobbek H, Haumann M. Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy. PLoS One 2017; 12:e0171039. [PMID: 28178309 PMCID: PMC5298270 DOI: 10.1371/journal.pone.0171039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/13/2017] [Indexed: 11/18/2022] Open
Abstract
Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.
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Affiliation(s)
- Peer Schrapers
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Julia Ilina
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christina M. Gregg
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Jae-Hun Jeoung
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Holger Dobbek
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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22
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Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo. J Bacteriol 2016; 198:2743-52. [PMID: 27457714 DOI: 10.1128/jb.00475-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/19/2016] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED The euryhaline cyanobacterium Synechococcus sp. strain PCC 7002 has an obligate requirement for exogenous vitamin B12 (cobalamin), but little is known about the roles of this compound in cyanobacteria. Bioinformatic analyses suggest that only the terminal enzyme in methionine biosynthesis, methionine synthase, requires cobalamin as a coenzyme in Synechococcus sp. strain PCC 7002. Methionine synthase (MetH) catalyzes the transfer of a methyl group from N(5)-methyl-5,6,7,8-tetrahydrofolate to l-homocysteine during l-methionine synthesis and uses methylcobalamin as an intermediate methyl donor. Numerous bacteria and plants alternatively employ a cobalamin-independent methionine synthase isozyme, MetE, that catalyzes the same methyl transfer reaction as MetH but uses N(5)-methyl-5,6,7,8-tetrahydrofolate directly as the methyl donor. The cobalamin auxotrophy of Synechococcus sp. strain PCC 7002 was complemented by using the metE gene from the closely related cyanobacterium Synechococcus sp. strain PCC 73109, which possesses genes for both methionine synthases. This result suggests that methionine biosynthesis is probably the sole use of cobalamin in Synechococcus sp. strain PCC 7002. Furthermore, a cobalamin-repressible gene expression system was developed in Synechococcus sp. strain PCC 7002 that was used to validate the presence of a cobalamin riboswitch in the promoter region of metE from Synechococcus sp. strain PCC 73109. This riboswitch acts as a cobalamin-dependent transcriptional attenuator for metE in that organism. IMPORTANCE Synechococcus sp. strain PCC 7002 is a cobalamin auxotroph because, like eukaryotic marine algae, it uses a cobalamin-dependent methionine synthase (MetH) for the final step of l-methionine biosynthesis but cannot synthesize cobalamin de novo Heterologous expression of metE, encoding cobalamin-independent methionine synthase, from Synechococcus sp. strain PCC 73109, relieved this auxotrophy and enabled the construction of a truly autotrophic Synechococcus sp. strain PCC 7002 more suitable for large-scale industrial applications. Characterization of a cobalamin riboswitch expands the genetic toolbox for Synechococcus sp. strain PCC 7002 by providing a cobalamin-repressible expression system.
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23
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Schrapers P, Mebs S, Goetzl S, Hennig SE, Dau H, Dobbek H, Haumann M. Axial Ligation and Redox Changes at the Cobalt Ion in Cobalamin Bound to Corrinoid Iron-Sulfur Protein (CoFeSP) or in Solution Characterized by XAS and DFT. PLoS One 2016; 11:e0158681. [PMID: 27384529 PMCID: PMC4934906 DOI: 10.1371/journal.pone.0158681] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/20/2016] [Indexed: 11/18/2022] Open
Abstract
A cobalamin (Cbl) cofactor in corrinoid iron-sulfur protein (CoFeSP) is the primary methyl group donor and acceptor in biological carbon oxide conversion along the reductive acetyl-CoA pathway. Changes of the axial coordination of the cobalt ion within the corrin macrocycle upon redox transitions in aqua-, methyl-, and cyano-Cbl bound to CoFeSP or in solution were studied using X-ray absorption spectroscopy (XAS) at the Co K-edge in combination with density functional theory (DFT) calculations, supported by metal content and cobalt redox level quantification with further spectroscopic methods. Calculation of the highly variable pre-edge X-ray absorption features due to core-to-valence (ctv) electronic transitions, XANES shape analysis, and cobalt-ligand bond lengths determination from EXAFS has yielded models for the molecular and electronic structures of the cobalt sites. This suggested the absence of a ligand at cobalt in CoFeSP in α-position where the dimethylbenzimidazole (dmb) base of the cofactor is bound in Cbl in solution. As main species, (dmb)CoIII(OH2), (dmb)CoII(OH2), and (dmb)CoIII(CH3) sites for solution Cbl and CoIII(OH2), CoII(OH2), and CoIII(CH3) sites in CoFeSP-Cbl were identified. Our data support binding of a serine residue from the reductive-activator protein (RACo) of CoFeSP to the cobalt ion in the CoFeSP-RACo protein complex that stabilizes Co(II). The absence of an α-ligand at cobalt not only tunes the redox potential of the cobalamin cofactor into the physiological range, but is also important for CoFeSP reactivation.
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Affiliation(s)
- Peer Schrapers
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
| | - Stefan Mebs
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
| | - Sebastian Goetzl
- Humboldt-Universität zu Berlin, Department of Biology, 10115, Berlin, Germany
| | - Sandra E. Hennig
- Humboldt-Universität zu Berlin, Department of Biology, 10115, Berlin, Germany
| | - Holger Dau
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Department of Biology, 10115, Berlin, Germany
| | - Michael Haumann
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
- * E-mail:
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24
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Gregg CM, Goetzl S, Jeoung JH, Dobbek H. AcsF Catalyzes the ATP-dependent Insertion of Nickel into the Ni,Ni-[4Fe4S] Cluster of Acetyl-CoA Synthase. J Biol Chem 2016; 291:18129-38. [PMID: 27382049 DOI: 10.1074/jbc.m116.731638] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Indexed: 12/16/2022] Open
Abstract
Acetyl-CoA synthase (ACS) catalyzes the reversible condensation of CO, CoA, and a methyl-cation to form acetyl-CoA at a unique Ni,Ni-[4Fe4S] cluster (the A-cluster). However, it was unknown which proteins support the assembly of the A-cluster. We analyzed the product of a gene from the cluster containing the ACS gene, cooC2 from Carboxydothermus hydrogenoformans, named AcsFCh, and showed that it acts as a maturation factor of ACS. AcsFCh and inactive ACS form a stable 2:1 complex that binds two nickel ions with higher affinity than the individual components. The nickel-bound ACS-AcsFCh complex remains inactive until MgATP is added, thereby converting inactive to active ACS. AcsFCh is a MinD-type ATPase and belongs to the CooC protein family, which can be divided into homologous subgroups. We propose that proteins of one subgroup are responsible for assembling the Ni,Ni-[4Fe4S] cluster of ACS, whereas proteins of a second subgroup mature the [Ni4Fe4S] cluster of carbon monoxide dehydrogenases.
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Affiliation(s)
- Christina M Gregg
- From the Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Sebastian Goetzl
- From the Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Jae-Hun Jeoung
- From the Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- From the Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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25
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Rettenmeier CA, Wadepohl H, Gade LH. Electronic structure and reactivity of nickel(i) pincer complexes: their aerobic transformation to peroxo species and site selective C-H oxygenation. Chem Sci 2016; 7:3533-3542. [PMID: 29997845 PMCID: PMC6007179 DOI: 10.1039/c5sc04644k] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/11/2016] [Indexed: 12/28/2022] Open
Abstract
The study is aimed at a deeper understanding of the electronic structure of the T-shaped nickel(i) complex [LigiPr(iso)Ni] (1b), bearing the iso-PyrrMeBox (bis(oxazolinylmethylidene)pyrrolidinido) pincer ligand, and its CO adduct [LigiPr(iso)Ni(CO)] (2b) as well as to provide insight into the mechanism of autoxidation of the different nickel peroxo species of this ligand type. CO was found to react reversibly with complex 1b resulting in the corresponding CO adduct 2b. The EPR data as well as the results of DFT modeling revealed significant differences in the electronic structure of 1b and 2b. Reaction of [LigPh(iso)Ni] and [LigiPr(iso)Ni] (1a and b) with dioxygen yielded the 1,2-μ-peroxo complexes [Lig(iso)NiO]23a and b which reacted with hydrogen peroxide to give the hydroperoxo complexes [Lig(iso)NiOOH] 5a and b. Thermal aerobic decomposition of the peroxo species 3a and 5a in the presence of O2 led to a C-H activation of the ligand at the benzylic position of the oxazoline ring forming diastereomeric cyclic peroxo complexes 6 and 6'. For the 1,2-μ-peroxo complex 3b the autoxidation of the pincer in the absence of O2 occurred at the tertiary C-H bond of the iPr-group and led to a selective formation of the terminal hydroxo complex [LigiPr(iso)NiOH] 7b and the cyclic alkoxy complex 8 in equimolar quantities, while the corresponding cyclic peroxo species 9 was formed along with 7b in the presence of oxygen. Whether or not O-O bond cleavage occurred in the generation of 9 was established upon performing labeling experiments which indicate that the transformation does not involve an initial O-O bond cleaving step. Based on these observations and a series of stoichiometric transformations a tentative proposal for the processes involved in the anaerobic and aerobic decomposition of 3b has been put forward. Finally, the nickel(ii) methyl complex [LigPh(iso)NiMe] 14 reacted with O2 to give the methylperoxo complex [LigPh(iso)NiOOMe] 15 which slowly converted to a mixture of near equal amounts of the formato and the hydroxo complexes, [LigPh(iso)NiOOCH] 16 and [LigPh(iso)NiOH] 7a, along with half an equivalent of methanol. The formato complex 16 itself decomposed at elevated temperatures to CO2, dihydrogen as well as the nickel(i) species 1a.
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Affiliation(s)
- Christoph A Rettenmeier
- Anorganisch-Chemisches Institut , University of Heidelberg , Im Neuenheimer Feld 270 , 69120 Heidelberg , Germany .
| | - Hubert Wadepohl
- Anorganisch-Chemisches Institut , University of Heidelberg , Im Neuenheimer Feld 270 , 69120 Heidelberg , Germany .
| | - Lutz H Gade
- Anorganisch-Chemisches Institut , University of Heidelberg , Im Neuenheimer Feld 270 , 69120 Heidelberg , Germany .
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26
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Sojo V, Herschy B, Whicher A, Camprubí E, Lane N. The Origin of Life in Alkaline Hydrothermal Vents. ASTROBIOLOGY 2016; 16:181-97. [PMID: 26841066 DOI: 10.1089/ast.2015.1406] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Over the last 70 years, prebiotic chemists have been very successful in synthesizing the molecules of life, from amino acids to nucleotides. Yet there is strikingly little resemblance between much of this chemistry and the metabolic pathways of cells, in terms of substrates, catalysts, and synthetic pathways. In contrast, alkaline hydrothermal vents offer conditions similar to those harnessed by modern autotrophs, but there has been limited experimental evidence that such conditions could drive prebiotic chemistry. In the Hadean, in the absence of oxygen, alkaline vents are proposed to have acted as electrochemical flow reactors, in which alkaline fluids saturated in H2 mixed with relatively acidic ocean waters rich in CO2, through a labyrinth of interconnected micropores with thin inorganic walls containing catalytic Fe(Ni)S minerals. The difference in pH across these thin barriers produced natural proton gradients with equivalent magnitude and polarity to the proton-motive force required for carbon fixation in extant bacteria and archaea. How such gradients could have powered carbon reduction or energy flux before the advent of organic protocells with genes and proteins is unknown. Work over the last decade suggests several possible hypotheses that are currently being tested in laboratory experiments, field observations, and phylogenetic reconstructions of ancestral metabolism. We analyze the perplexing differences in carbon and energy metabolism in methanogenic archaea and acetogenic bacteria to propose a possible ancestral mechanism of CO2 reduction in alkaline hydrothermal vents. Based on this mechanism, we show that the evolution of active ion pumping could have driven the deep divergence of bacteria and archaea.
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Affiliation(s)
- Victor Sojo
- 1 Department of Genetics, Evolution and Environment, University College London , London, UK
- 2 CoMPLEX, University College London , London, UK
| | - Barry Herschy
- 1 Department of Genetics, Evolution and Environment, University College London , London, UK
| | - Alexandra Whicher
- 1 Department of Genetics, Evolution and Environment, University College London , London, UK
| | - Eloi Camprubí
- 1 Department of Genetics, Evolution and Environment, University College London , London, UK
| | - Nick Lane
- 1 Department of Genetics, Evolution and Environment, University College London , London, UK
- 2 CoMPLEX, University College London , London, UK
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Ammam F, Tremblay PL, Lizak DM, Zhang T. Effect of tungstate on acetate and ethanol production by the electrosynthetic bacterium Sporomusa ovata. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:163. [PMID: 27493685 PMCID: PMC4973070 DOI: 10.1186/s13068-016-0576-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/27/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microbial electrosynthesis (MES) and gas fermentation are bioenergy technologies in which a microbial catalyst reduces CO2 into organic carbon molecules with electrons from the cathode of a bioelectrochemical system or from gases such as H2. The acetogen Sporomusa ovata has the capacity of reducing CO2 into commodity chemicals by both gas fermentation and MES. Acetate is often the only product generated by S. ovata during autotrophic growth. RESULTS In this study, trace elements in S. ovata growth medium were optimized to improve MES and gas fermentation productivity. Augmenting tungstate concentration resulted in a 2.9-fold increase in ethanol production by S. ovata during H2:CO2-dependent growth. It also promoted electrosynthesis of ethanol in a S. ovata-driven MES reactor and increased acetate production 4.4-fold compared to unmodified medium. Furthermore, fatty acids propionate and butyrate were successfully converted to their corresponding alcohols 1-propanol and 1-butanol by S. ovata during gas fermentation. Increasing tungstate concentration enhanced conversion efficiency for both propionate and butyrate. Gene expression analysis suggested that tungsten-containing aldehyde ferredoxin oxidoreductases (AORs) and a tungsten-containing formate dehydrogenase (FDH) were involved in the improved biosynthesis of acetate, ethanol, 1-propanol, and 1-butanol. AORs and FDH contribute to the fatty acids re-assimilation pathway and the Wood-Ljungdahl pathway, respectively. CONCLUSIONS This study presented here shows that optimization of microbial catalyst growth medium can improve productivity and lead to the biosynthesis of different products by gas fermentation and MES. It also provides insights on the metabolism of biofuels production in acetogens and demonstrates that S. ovata has an important untapped metabolic potential for the production of other chemicals than acetate via CO2-converting bioprocesses including MES.
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Affiliation(s)
- Fariza Ammam
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Pier-Luc Tremblay
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070 People’s Republic of China
| | - Dawid M. Lizak
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Tian Zhang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070 People’s Republic of China
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28
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He Z, Yu Y, Wang D, Tang J, Chen J, Song S. Photocatalytic reduction of carbon dioxide using iodine-doped titanium dioxide with high exposed {001} facets under visible light. RSC Adv 2016. [DOI: 10.1039/c5ra26761g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Iodine-doped titanium dioxide nanosheets with high exposed {001} facets (IFTO) were synthesized by a two-step hydrothermal treatment followed by calcination at 350 °C.
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Affiliation(s)
- Zhiqiao He
- College of Biological and Environmental Engineering
- Zhejiang University of Technology
- Hangzhou 310032
- People's Republic of China
| | - Yan Yu
- College of Biological and Environmental Engineering
- Zhejiang University of Technology
- Hangzhou 310032
- People's Republic of China
| | - Da Wang
- College of Biological and Environmental Engineering
- Zhejiang University of Technology
- Hangzhou 310032
- People's Republic of China
| | - Juntao Tang
- College of Biological and Environmental Engineering
- Zhejiang University of Technology
- Hangzhou 310032
- People's Republic of China
| | - Jianmeng Chen
- College of Biological and Environmental Engineering
- Zhejiang University of Technology
- Hangzhou 310032
- People's Republic of China
| | - Shuang Song
- College of Biological and Environmental Engineering
- Zhejiang University of Technology
- Hangzhou 310032
- People's Republic of China
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29
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Miller DL, Boro BJ, Grubel K, Helm ML, Appel AM. Synthesis and Characterization of a Triphos Ligand Derivative and the Corresponding Pd
II
Complexes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500791] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Deanna L. Miller
- Pacific Northwest National Laboratory, P. O. Box 999, MS K2‐57, Richland, WA 99352, USA, http://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7812
| | - Brian J. Boro
- Pacific Northwest National Laboratory, P. O. Box 999, MS K2‐57, Richland, WA 99352, USA, http://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7812
| | - Katarzyna Grubel
- Pacific Northwest National Laboratory, P. O. Box 999, MS K2‐57, Richland, WA 99352, USA, http://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7812
| | - Monte L. Helm
- Pacific Northwest National Laboratory, P. O. Box 999, MS K2‐57, Richland, WA 99352, USA, http://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7812
| | - Aaron M. Appel
- Pacific Northwest National Laboratory, P. O. Box 999, MS K2‐57, Richland, WA 99352, USA, http://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7812
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Wang VCC, Islam STA, Can M, Ragsdale SW, Armstrong FA. Investigations by Protein Film Electrochemistry of Alternative Reactions of Nickel-Containing Carbon Monoxide Dehydrogenase. J Phys Chem B 2015; 119:13690-7. [PMID: 26176986 DOI: 10.1021/acs.jpcb.5b03098] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein film electrochemistry has been used to investigate reactions of highly active nickel-containing carbon monoxide dehydrogenases (CODHs). When attached to a pyrolytic graphite electrode, these enzymes behave as reversible electrocatalysts, displaying CO2 reduction or CO oxidation at minimal overpotential. The O2 sensitivity of CODH is suppressed by adding cyanide, a reversible inhibitor of CO oxidation, or by raising the electrode potential. Reduction of N2O, isoelectronic with CO2, is catalyzed by CODH, but the reaction is sluggish, despite a large overpotential, and results in inactivation. Production of H2 and formate under highly reducing conditions is consistent with calculations predicting that a nickel-hydrido species might be formed, but the very low rates suggest that such a species is not on the main catalytic pathway.
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Affiliation(s)
- Vincent C-C Wang
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Shams T A Islam
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - Fraser A Armstrong
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
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31
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Riordan CG. Organometallic Chemistry. Catalysis by nickel in its high oxidation state. Science 2015; 347:1203-4. [PMID: 25766220 DOI: 10.1126/science.aaa7553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Charles G Riordan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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Peterson SM, Helm ML, Appel AM. Nickel complexes of a binucleating ligand derived from an SCS pincer. Dalton Trans 2015; 44:747-52. [DOI: 10.1039/c4dt02718c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new heterobimetallic complex contains NiII in an SCS pincer and lithium in an ether loop, bridged by bromide.
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33
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Allen KD, Wang SC. Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2135-44. [PMID: 25224746 DOI: 10.1016/j.bbapap.2014.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/05/2014] [Accepted: 09/07/2014] [Indexed: 10/24/2022]
Abstract
Natural products containing carbon-phosphorus bonds elicit important bioactivity in many organisms. l-Phosphinothricin contains the only known naturally-occurring carbon-phosphorus-carbon bond linkage. In actinomycetes, the cobalamin-dependent radical S-adenosyl-l-methionine (SAM) methyltransferase PhpK catalyzes the formation of the second C-P bond to generate the complete C-P-C linkage in phosphinothricin. Here we use electron paramagnetic resonance and nuclear magnetic resonance spectroscopies to characterize and demonstrate the activity of a cobalamin-dependent radical SAM methyltransferase denoted SD_1168 from Shewanella denitrificans OS217, a marine bacterium that has not been reported to synthesize phosphinothricin. Recombinant, refolded, and reconstituted SD_1168 binds a four-iron, four-sulfur cluster that interacts with SAM and cobalamin. In the presence of SAM, a reductant, and methylcobalamin, SD_1168 surprisingly catalyzes the P-methylation of N-acetyl-demethylphosphinothricin and demethylphosphinothricin to produce N-acetyl-phosphinothricin and phosphinothricin, respectively. In addition, this enzyme is active in the absence of methylcobalamin if the strong reductant titanium (III) citrate and hydroxocobalamin are provided. When incubated with [methyl-(13)C] cobalamin and titanium citrate, both [methyl-(13)C] and unlabeled N-acetylphosphinothricin are produced. Our results suggest that SD_1168 catalyzes P-methylation using radical SAM-dependent chemistry with cobalamin as a coenzyme. In light of recent genomic information, the discovery of this P-methyltransferase suggests that S. denitrificans produces a phosphinate natural product.
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Affiliation(s)
- Kylie D Allen
- School of Molecular Biosciences, College of Veterinary Medicine, PO Box 647520, Washington State University, Pullman, WA 99164-7520, USA.
| | - Susan C Wang
- School of Molecular Biosciences, College of Veterinary Medicine, PO Box 647520, Washington State University, Pullman, WA 99164-7520, USA.
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Evidence for a hexaheteromeric methylenetetrahydrofolate reductase in Moorella thermoacetica. J Bacteriol 2014; 196:3303-14. [PMID: 25002540 DOI: 10.1128/jb.01839-14] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Moorella thermoacetica can grow with H₂ and CO₂, forming acetic acid from 2 CO₂ via the Wood-Ljungdahl pathway. All enzymes involved in this pathway have been characterized to date, except for methylenetetrahydrofolate reductase (MetF). We report here that the M. thermoacetica gene that putatively encodes this enzyme, metF, is part of a transcription unit also containing the genes hdrCBA, mvhD, and metV. MetF copurified with the other five proteins encoded in the unit in a hexaheteromeric complex with an apparent molecular mass in the 320-kDa range. The 40-fold-enriched preparation contained per mg protein 3.1 nmol flavin adenine dinucleotide (FAD), 3.4 nmol flavin mononucleotide (FMN), and 110 nmol iron, almost as predicted from the primary structure of the six subunits. It catalyzed the reduction of methylenetetrahydrofolate with reduced benzyl viologen but not with NAD(P)H in either the absence or presence of oxidized ferredoxin. It also catalyzed the reversible reduction of benzyl viologen with NADH (diaphorase activity). Heterologous expression of the metF gene in Escherichia coli revealed that the subunit MetF contains one FMN rather than FAD. MetF exhibited 70-fold-higher methylenetetrahydrofolate reductase activity with benzyl viologen when produced together with MetV, which in part shows sequence similarity to MetF. Heterologously produced HdrA contained 2 FADs and had NAD-specific diaphorase activity. Our results suggested that the physiological electron donor for methylenetetrahydrofolate reduction in M. thermoacetica is NADH and that the exergonic reduction of methylenetetrahydrofolate with NADH is coupled via flavin-based electron bifurcation with the endergonic reduction of an electron acceptor, whose identity remains unknown.
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35
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Weidenbach K, Ehlers C, Schmitz RA. The transcriptional activator NrpA is crucial for inducing nitrogen fixation in Methanosarcina mazei Gö1 under nitrogen-limited conditions. FEBS J 2014; 281:3507-22. [PMID: 24930989 DOI: 10.1111/febs.12876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/05/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
Abstract
With the aim of unraveling their potential involvement in the regulation of nitrogen metabolism in Methanosarcina mazei strain Gö1, we characterized five genes that are differentially transcribed in response to changing nitrogen availability and encoding putative transcriptional regulators. Study of the respective mutant strains under nitrogen-limited conditions revealed a growth delay for M. mazei MM0444::pac and MM1708::pac, and strongly reduced diazotrophic growth for MM0872::pac, whereas the absence of MM2441 or MM2525 did not affect growth behaviour. Transcriptome analyses further demonstrated that only MM1708 - encoding a CxxCG zinc finger protein - plays a regulatory role in nitrogen metabolism, most likely by specifically enhancing transcription of the N2 fixation (nif) operon under nitrogen-limited conditions. In agreement with this, a palindromic binding motif was predicted in silico in the nifH promoter region, nine nucleotides upstream of the BRE box, and confirmed to bind purified maltose-binding protein-MM1708 by electromobility shift assays. As MM1708 itself is under the control of the global nitrogen repressor NrpR, this adds a secondary level to the transcriptional regulation of the nif genes, and is most likely crucial for maximal nif induction under nitrogen-limited conditions. This is in accordance with the finding that protein expression of NifH is highly reduced in the absence of MM1708 under nitrogen-limited conditions. On the basis of our findings, we hypothesize that, in M. mazei, nitrogen fixation is controlled by a hierarchical network of two transcriptional regulators, the global nitrogen repressor NrpR, and the newly identified activator NrpA (MM1708), thereby providing tight control of N2 fixation.
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36
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Horn B, Limberg C, Herwig C, Braun B. Three-Coordinate Nickel(II) and Nickel(I) Thiolate Complexes Based on the β-Diketiminate Ligand System. Inorg Chem 2014; 53:6867-74. [DOI: 10.1021/ic500698v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bettina Horn
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Christian Limberg
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Christian Herwig
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Beatrice Braun
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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37
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Ni Y, Hagedoorn PL, Xu JH, Arends IW, Hollmann F. Pyrococcus furiosus-mediated reduction of conjugated carboxylic acids: Towards using syngas as reductant. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Yoo C, Oh S, Kim J, Lee Y. Transmethylation of a four-coordinate nickel(i) monocarbonyl species with methyl iodide. Chem Sci 2014. [DOI: 10.1039/c4sc01089b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The reaction of a nickel(i) carbonyl species with CH3I revealed the formation of (PNP)NiCOCH3 which differs from its zerovalent congener.
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Affiliation(s)
- Changho Yoo
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701, Republic of Korea
| | - Seohee Oh
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701, Republic of Korea
| | - Jin Kim
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701, Republic of Korea
| | - Yunho Lee
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701, Republic of Korea
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39
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Wang V, Ragsdale SW, Armstrong FA. Investigations of the efficient electrocatalytic interconversions of carbon dioxide and carbon monoxide by nickel-containing carbon monoxide dehydrogenases. Met Ions Life Sci 2014; 14:71-97. [PMID: 25416391 PMCID: PMC4261625 DOI: 10.1007/978-94-017-9269-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Carbon monoxide dehydrogenases (CODH) play an important role in utilizing carbon monoxide (CO) or carbon dioxide (CO2) in the metabolism of some microorganisms. Two distinctly different types of CODH are distinguished by the elements constituting the active site. A Mo-Cu containing CODH is found in some aerobic organisms, whereas a Ni-Fe containing CODH (henceforth simply Ni-CODH) is found in some anaerobes. Two members of the simplest class (IV) of Ni-CODH behave as efficient, reversible electrocatalysts of CO2/CO interconversion when adsorbed on a graphite electrode. Their intense electroactivity sets an important benchmark for the standard of performance at which synthetic molecular and material electrocatalysts comprised of suitably attired abundant first-row transition elements must be able to operate. Investigations of CODHs by protein film electrochemistry (PFE) reveal how the enzymes respond to the variable electrode potential that can drive CO2/CO interconversion in each direction, and identify the potential thresholds at which different small molecules, both substrates and inhibitors, enter or leave the catalytic cycle. Experiments carried out on a much larger (Class III) enzyme CODH/ACS, in which CODH is complexed tightly with acetyl-CoA synthase, show that some of these characteristics are retained, albeit with much slower rates of interfacial electron transfer, attributable to the difficulty in making good electronic contact at the electrode. The PFE results complement and clarify investigations made using spectroscopic investigations.
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40
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Wang VCC, Ragsdale SW, Armstrong FA. Investigations of two bidirectional carbon monoxide dehydrogenases from Carboxydothermus hydrogenoformans by protein film electrochemistry. Chembiochem 2013; 14:1845-51. [PMID: 24002936 DOI: 10.1002/cbic.201300270] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 11/08/2022]
Abstract
Carbon monoxide dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO2 . Several small molecules or ions are inhibitors and probes for different oxidation states of the unusual [Ni-4 Fe-4 S] cluster that forms the active site. The actions of these small probes on two enzymes-CODH ICh and CODH IICh -produced by Carboxydothermus hydrogenoformans have been studied by protein film voltammetry to compare their behaviour and to establish general characteristics. Whereas CODH ICh is, so far, the better studied of the two isozymes in terms of its electrocatalytic properties, it is CODH IICh that has been characterised by X-ray crystallography. The two isozymes, which share 58.3% sequence identity and 73.9% sequence similarity, show similar patterns of behaviour with regard to selective inhibition of CO2 reduction by CO (product) and cyanate, potent and selective inhibition of CO oxidation by cyanide, and the action of sulfide, which promotes oxidative inactivation of the enzyme. For both isozymes, rates of binding of substrate analogues CN(-) (for CO) and NCO(-) (for CO2 ) are orders of magnitude lower than turnover, a feature that is clearly revealed through hysteresis of cyclic voltammetry. Inhibition by CN(-) and CO is much stronger for CODH IICh than for CODH ICh, a property that has relevance for applying these enzymes as model catalysts in solar-driven CO2 reduction.
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Affiliation(s)
- Vincent C-C Wang
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR (UK)
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Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IAC, Allen JF, Lane N, Martin WF. Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130088. [PMID: 23754820 PMCID: PMC3685469 DOI: 10.1098/rstb.2013.0088] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood-Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent-ocean interface via the ATP synthase, (iii) harnessing of Na(+) gradients generated by H(+)/Na(+) antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type 'reduced iron → reduced carbon' at the beginning of bioenergetic evolution.
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Affiliation(s)
- Filipa L. Sousa
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Thorsten Thiergart
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giddy Landan
- Institute of Genomic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - John F. Allen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
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Wang PH, Bruschi M, De Gioia L, Blumberger J. Uncovering a dynamically formed substrate access tunnel in carbon monoxide dehydrogenase/acetyl-CoA synthase. J Am Chem Soc 2013; 135:9493-502. [PMID: 23713976 DOI: 10.1021/ja403110s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The transport of small ligands to active sites of proteins is the basis of vital processes in biology such as enzymatic catalysis and cell signaling, but also of more destructive ones including enzyme inhibition and oxidative damage. Here, we show how a diffusion-reaction model solved by means of molecular dynamics and density functional theory calculations provides novel insight into the transport of small ligands in proteins. In particular, we unravel the existence of an elusive, dynamically formed gas channel, which CO2 takes to diffuse from the solvent to the active site (C-cluster) of the bifunctional multisubunit enzyme complex carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). Two cavities forming this channel are temporarily created by protein fluctuations and are not apparent in the X-ray structures. The ligand transport is controlled by two residues at the end of this tunnel, His113 and His116, and occurs on the same time scale on which chemical binding to the active site takes place (0.1-1 ms), resulting in an overall binding rate on the second time scale. We find that upon reduction of CO2 to CO, the newly formed Fe-hydroxy ligand greatly strengthens the hydrogen-bond network, preventing CO from exiting the protein through the same way that CO2 takes to enter the protein. This is the basis for directional transport of CO from the production site (C-cluster of CODH subunit) to the utilization site (A-cluster of ACS subunit). In view of these results, a general picture emerges of how large proteins guide small ligands toward their active sites.
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Affiliation(s)
- Po-hung Wang
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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Abstract
Harnessing energy as ion gradients across membranes is as universal as the genetic code. We leverage new insights into anaerobe metabolism to propose geochemical origins that account for the ubiquity of chemiosmotic coupling, and Na(+)/H(+) transporters in particular. Natural proton gradients acting across thin FeS walls within alkaline hydrothermal vents could drive carbon assimilation, leading to the emergence of protocells within vent pores. Protocell membranes that were initially leaky would eventually become less permeable, forcing cells dependent on natural H(+) gradients to pump Na(+) ions. Our hypothesis accounts for the Na(+)/H(+) promiscuity of bioenergetic proteins, as well as the deep divergence between bacteria and archaea.
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Gencic S, Kelly K, Ghebreamlak S, Duin EC, Grahame DA. Different Modes of Carbon Monoxide Binding to Acetyl-CoA Synthase and the Role of a Conserved Phenylalanine in the Coordination Environment of Nickel. Biochemistry 2013; 52:1705-16. [DOI: 10.1021/bi3016718] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Simonida Gencic
- Department of Biochemistry and
Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Kayla Kelly
- Holton-Arms School, Bethesda, Maryland 20817, United States
| | - Selamawit Ghebreamlak
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Evert C. Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - David A. Grahame
- Department of Biochemistry and
Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
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46
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Wächtler M, Guthmuller J, González L, Dietzek B. Analysis and characterization of coordination compounds by resonance Raman spectroscopy. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.02.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Tavares AFN, Nobre LS, Saraiva LM. A role for reactive oxygen species in the antibacterial properties of carbon monoxide-releasing molecules. FEMS Microbiol Lett 2012; 336:1-10. [PMID: 22774863 DOI: 10.1111/j.1574-6968.2012.02633.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 12/24/2022] Open
Abstract
Carbon monoxide-releasing molecules (CO-RMs) are, in general, transition metal carbonyl complexes that liberate controlled amounts of CO. In animal models, CO-RMs have been shown to reduce myocardial ischaemia, inflammation and vascular dysfunction, and to provide a protective effect in organ transplantation. Moreover, CO-RMs are bactericides that kill both Gram-positive and Gram-negative bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa. Herein are reviewed the microbial genetic and biochemical responses associated with CO-RM-mediated cell death. Particular emphasis is given to the data revealing that CO-RMs induce the generation of reactive oxygen species (ROS), which contribute to the antibacterial activity of these compounds.
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Affiliation(s)
- Ana Filipa N Tavares
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Douglas CD, Dias AV, Zamble DB. The metal selectivity of a short peptide maquette imitating the high-affinity metal-binding site of E. coli HypB. Dalton Trans 2012; 41:7876-8. [DOI: 10.1039/c2dt30132f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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