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Hong Dao NP, Nguyen TH, Watari T, Hatamoto M, Tan NM, Huong NL, Yamaguchi T. Investigate the anaerobic degradation of high-acetone latex wastewater with magnetite supplement. CHEMOSPHERE 2023; 339:139626. [PMID: 37487980 DOI: 10.1016/j.chemosphere.2023.139626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/24/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This study evaluated the effects of acetone on the anaerobic degradation of synthetic latex wastewater, which was simulated from the wastewater of the deproteinized natural rubber production process, including latex, acetate, propionate, and acetone as the main carbon sources, at a batch scale in 5 cycles of a total of 60 days. Fe3O4 was applied to accelerate the treatment performance from cycle 3. Acetone was added in concentration ranges of 0%, 0.05%, 0.1%, 0.15%-included latex, and 0.15%-free latex (w/v). In the Fe3O4-free cycles, for latex-added vials, soluble chemical oxygen demand (sCOD) was removed at 43.20%, 43.20%, and 12.65%, corresponding to the input acetone concentrations varying from 0.05% to 0.15%, indicating the interference of acetone for COD reduction. After adding Fe3O4, all flasks reported a significant increase in COD removal efficiency, especially for acetone-only and latex-only vials, from 36.9% to 14.30%-42.95% and 83.20%, respectively. Other highlighted results of COD balance showed that Fe3O4 involvement improved the degradation process of acetate, propionate, acetone, and the other COD parts, including the intermediate products of latex reduction. Besides, during the whole batch process, the order of reduction priority of the carbon sources in the synthetic wastewater was acetate, propionate and acetone. We also found that the acetate concentration appeared to be strongly related to reducing other carbon sources in natural rubber wastewater. Microbial community analysis revealed that protein-degrading bacteria Bacteroidetes vadinHA17 and Proteinniphilum and methylotrophic methanogens might play key roles in treating simulated deproteinized-natural-rubber wastewater.
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Affiliation(s)
- Nguyen Pham Hong Dao
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Thu Huong Nguyen
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan; School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam.
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Nguyen Minh Tan
- Institute for R&D of Natural Products, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam
| | - Nguyen Lan Huong
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan; Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan; School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam
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2
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Wu Y, Wu J, Wu Z, Zhou J, Zhou L, Lu Y, Liu X, Wu W. Groundwater contaminated with short-chain chlorinated paraffins and microbial responses. WATER RESEARCH 2021; 204:117605. [PMID: 34488140 DOI: 10.1016/j.watres.2021.117605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The vertical migrations of toxic and persistent short-chain chlorinated paraffins (SCCPs) in soils as well as the microbial responses have been reported, however, there is a paucity of data on the resulting groundwater contamination. Here, we determined the concentration and congener profile of SCCPs in the groundwater beneath a production plant of chlorinated paraffins (CPs) and characterized the microbial community to explore their responses to SCCPs. Results showed that SCCPs ranged from not detected to 70.3 μg/L, with C13-CPs (11.2-65.8%) and Cl7-CPs (27.2-50.6%), in mass ratio, as the dominant groups. Similar to the distribution pattern in soils, SCCPs in groundwater were distributed in hotspot pattern. CP synthesis was the source of SCCPs in groundwater and the entire contamination plume significantly migrated downgradient, while there was an apparent hysteresis of C13-CP migration. Groundwater microbial community was likely shaped by both hydrogeological condition (pH and depth) and SCCPs. Specifically, the microbial community responded to the contamination by forming a co-occurrence network with "small world" feature, where Desulfobacca, Desulfomonile, Ferritrophicum, Methylomonas, Syntrophobacter, Syntrophorhabdus, Syntrophus, and Thermoanaerobaculum were the keystone taxa. Furthermore, the interrelations between bacterial taxa and SCCPs indicated that the microbial community might cooperate to achieve the dechlorination and mineralization of SCCPs through either anaerobic organohalide respiration mainly functioned by the keystone taxa, or cometabolic degradation processes functioned by Aquabacterium and Hydrogenophaga. Results of this study would provide a better understanding of the environmental behavior and ecological effects of SCCPs in groundwater systems.
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Affiliation(s)
- Yingxin Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Jiahui Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Zhuohao Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Jingyan Zhou
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Lingli Zhou
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Yang Lu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Xiaowen Liu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Wencheng Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China.
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3
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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4
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Hammler D, Marx A, Zumbusch A. Fluorescence-Lifetime-Sensitive Probes for Monitoring ATP Cleavage. Chemistry 2018; 24:15329-15335. [PMID: 30070405 DOI: 10.1002/chem.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/14/2022]
Abstract
Adenosine triphosphate (ATP) probes modified with fluorescence dyes that change their fluorescence properties upon cleavage are an interesting tool for monitoring enzymatic ATP turnover. As a readout parameter, fluorescence lifetime is attractive because it is nearly independent of concentration. In our study, we synthesised and investigated fifteen different ATP analogues, in which the fluorophores were attached to the γ-phosphate of ATP. All analogues showed distinctly different fluorescence lifetimes compared to the corresponding values of the free fluorophores. Both increases and decreases in fluorescence lifetime were observed upon attachment to ATP. To shed light on the photophysical processes governing the lifetime changes, we performed photoelectron spectroscopy in air (PESA) to determine HOMO energy levels and time-resolved fluorescence spectroscopy to obtain rate constants. We present evidence that fluorescence quenching in the compounds tested is dynamic and attributed to photoinduced electron transfer (PET), whereas fluorescence lifetime increases are caused by stacking interactions between chromophore and the nucleobase reducing non-radiative relaxation. Finally, we demonstrate that enzymatic cleavage of the ATP analogues presented can be followed by continuous monitoring of fluorescence lifetime changes.
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Affiliation(s)
- Daniel Hammler
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied Photonics, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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Wanat P, Kasprzyk R, Kopcial M, Sikorski PJ, Strzelecka D, Jemielity J, Kowalska J. ExciTides: NTP-derived probes for monitoring pyrophosphatase activity based on excimer-to-monomer transitions. Chem Commun (Camb) 2018; 54:9773-9776. [PMID: 30105342 DOI: 10.1039/c8cc04968h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a new type of nucleotide-derived fluorescent probe designed for monitoring pyrophosphatase activity based on excimer-to-monomer transitions, called ExciTide. The nucleotides were designed with two self-interacting dye moieties and synthesised using copper-catalysed azide-alkyne cycloaddition click chemistry. We applied these probes for enzyme activity monitoring and inhibitor evaluation. Some of the probes permeated into living cells, yielding interesting prospects for future applications.
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Affiliation(s)
- Przemyslaw Wanat
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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7
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Ermert S, Marx A, Hacker SM. Phosphate-Modified Nucleotides for Monitoring Enzyme Activity. Top Curr Chem (Cham) 2017; 375:28. [PMID: 28251563 DOI: 10.1007/s41061-017-0117-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/30/2017] [Indexed: 02/07/2023]
Abstract
Nucleotides modified at the terminal phosphate position have been proven to be interesting entities to study the activity of a variety of different protein classes. In this chapter, we present various types of modifications that were attached as reporter molecules to the phosphate chain of nucleotides and briefly describe the chemical reactions that are frequently used to synthesize them. Furthermore, we discuss a variety of applications of these molecules. Kinase activity, for instance, was studied by transfer of a phosphate modified with a reporter group to the target proteins. This allows not only studying the activity of kinases, but also identifying their target proteins. Moreover, kinases can also be directly labeled with a reporter at a conserved lysine using acyl-phosphate probes. Another important application for phosphate-modified nucleotides is the study of RNA and DNA polymerases. In this context, single-molecule sequencing is made possible using detection in zero-mode waveguides, nanopores or by a Förster resonance energy transfer (FRET)-based mechanism between the polymerase and a fluorophore-labeled nucleotide. Additionally, fluorogenic nucleotides that utilize an intramolecular interaction between a fluorophore and the nucleobase or an intramolecular FRET effect have been successfully developed to study a variety of different enzymes. Finally, also some novel techniques applying electron paramagnetic resonance (EPR)-based detection of nucleotide cleavage or the detection of the cleavage of fluorophosphates are discussed. Taken together, nucleotides modified at the terminal phosphate position have been applied to study the activity of a large diversity of proteins and are valuable tools to enhance the knowledge of biological systems.
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Affiliation(s)
- Susanne Ermert
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany.
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Brown ME, Mukhopadhyay A, Keasling JD. Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol. ACS Synth Biol 2016; 5:1485-1496. [PMID: 27403844 DOI: 10.1021/acssynbio.6b00115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report an engineered strain of Escherichia coli that catabolizes the carbonaceous component of the extremely toxic chemical warfare agent sarin. Enzymatic decomposition of sarin generates isopropanol waste that, with this engineered strain, is then transformed into acetyl-CoA by enzymatic conversion with a key reaction performed by the acetone carboxylase complex (ACX). We engineered the heterologous expression of the ACX complex from Xanthobacter autotrophicus PY2 to match the naturally occurring subunit stoichiometry and purified the recombinant complex from E. coli for biochemical analysis. Incorporating this ACX complex and enzymes from diverse organisms, we introduced an isopropanol degradation pathway in E. coli, optimized induction conditions, and decoupled enzyme expression to probe pathway bottlenecks. Our engineered E. coli consumed 65% of isopropanol compared to no-cell controls and was able to grow on isopropanol as a sole carbon source. In the process, reconstitution of this large ACX complex (370 kDa) in a system naïve to its structural and mechanistic requirements allowed us to study this otherwise cryptic enzyme in more detail than would have been possible in the less genetically tractable native Xanthobacter system.
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Affiliation(s)
- Margaret E. Brown
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Aindrila Mukhopadhyay
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jay D. Keasling
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle, DK2970-Hørsholm, Denmark
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9
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Frey J, Rusche H, Schink B, Schleheck D. Cloning, functional expression and characterization of a bifunctional 3-hydroxybutanal dehydrogenase /reductase involved in acetone metabolism by Desulfococcus biacutus. BMC Microbiol 2016; 16:280. [PMID: 27884109 PMCID: PMC5123277 DOI: 10.1186/s12866-016-0899-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The strictly anaerobic, sulfate-reducing bacterium Desulfococcus biacutus can utilize acetone as sole carbon and energy source for growth. Whereas in aerobic and nitrate-reducing bacteria acetone is activated by carboxylation with CO2 to acetoacetate, D. biacutus involves CO as a cosubstrate for acetone activation through a different, so far unknown pathway. Proteomic studies indicated that, among others, a predicted medium-chain dehydrogenase/reductase (MDR) superfamily, zinc-dependent alcohol dehydrogenase (locus tag DebiaDRAFT_04514) is specifically and highly produced during growth with acetone. Results The MDR gene DebiaDRAFT_04514 was cloned and overexpressed in E. coli. The purified recombinant protein required zinc as cofactor, and accepted NADH/NAD+ but not NADPH/NADP+ as electron donor/acceptor. The pH optimum was at pH 8, and the temperature optimum at 45 °C. Highest specific activities were observed for reduction of C3 - C5-aldehydes with NADH, such as propanal to propanol (380 ± 15 mU mg−1 protein), butanal to butanol (300 ± 24 mU mg−1), and 3-hydroxybutanal to 1,3-butanediol (248 ± 60 mU mg−1), however, the enzyme also oxidized 3-hydroxybutanal with NAD+ to acetoacetaldehyde (83 ± 18 mU mg−1). Conclusion The enzyme might play a key role in acetone degradation by D. biacutus, for example as a bifunctional 3-hydroxybutanal dehydrogenase/reductase. Its recombinant production may represent an important step in the elucidation of the complete degradation pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0899-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jasmin Frey
- Department of Biology, University of Konstanz, Postbox 649, D-78457, Konstanz, Germany
| | - Hendrik Rusche
- Department of Biology, University of Konstanz, Postbox 649, D-78457, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Postbox 649, D-78457, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Postbox 649, D-78457, Konstanz, Germany.
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Rajendran M, Dane E, Conley J, Tantama M. Imaging Adenosine Triphosphate (ATP). THE BIOLOGICAL BULLETIN 2016; 231:73-84. [PMID: 27638696 PMCID: PMC5063237 DOI: 10.1086/689592] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Adenosine triphosphate (ATP) is a universal mediator of metabolism and signaling across unicellular and multicellular species. There is a fundamental interdependence between the dynamics of ATP and the physiology that occurs inside and outside the cell. Characterizing and understanding ATP dynamics provide valuable mechanistic insight into processes that range from neurotransmission to the chemotaxis of immune cells. Therefore, we require the methodology to interrogate both temporal and spatial components of ATP dynamics from the subcellular to the organismal levels in live specimens. Over the last several decades, a number of molecular probes that are specific to ATP have been developed. These probes have been combined with imaging approaches, particularly optical microscopy, to enable qualitative and quantitative detection of this critical molecule. In this review, we survey current examples of technologies available for visualizing ATP in living cells, and identify areas where new tools and approaches are needed to expand our capabilities.
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Affiliation(s)
- Megha Rajendran
- Department of Chemistry, Purdue University, 560 Oval Drive, Box 68, West Lafayette, Indiana 47907; and
| | - Eric Dane
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 76-211, Cambridge, Massachusetts 02139
| | - Jason Conley
- Department of Chemistry, Purdue University, 560 Oval Drive, Box 68, West Lafayette, Indiana 47907; and
| | - Mathew Tantama
- Department of Chemistry, Purdue University, 560 Oval Drive, Box 68, West Lafayette, Indiana 47907; and
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Heider J, Schühle K, Frey J, Schink B. Activation of Acetone and Other Simple Ketones in Anaerobic Bacteria. J Mol Microbiol Biotechnol 2016; 26:152-64. [PMID: 26958851 DOI: 10.1159/000441500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Acetone and other ketones are activated for subsequent degradation through carboxylation by many nitrate-reducing, phototrophic, and obligately aerobic bacteria. Acetone carboxylation leads to acetoacetate, which is subsequently activated to a thioester and degraded via thiolysis. Two different types of acetone carboxylases have been described, which require either 2 or 4 ATP equivalents as an energy supply for the carboxylation reaction. Both enzymes appear to combine acetone enolphosphate with carbonic phosphate to form acetoacetate. A similar but more complex enzyme is known to carboxylate the aromatic ketone acetophenone, a metabolic intermediate in anaerobic ethylbenzene metabolism in denitrifying bacteria, with simultaneous hydrolysis of 2 ATP to 2 ADP. Obligately anaerobic sulfate-reducing bacteria activate acetone to a four-carbon compound as well, but via a different process than bicarbonate- or CO2-dependent carboxylation. The present evidence indicates that either carbon monoxide or a formyl residue is used as a cosubstrate, and that the overall ATP expenditure of this pathway is substantially lower than in the known acetone carboxylase reactions.
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Affiliation(s)
- Johann Heider
- Laboratory of Microbiology, LOEWE Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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12
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Hacker SM, Buntz A, Zumbusch A, Marx A. Direct Monitoring of Nucleotide Turnover in Human Cell Extracts and Cells by Fluorogenic ATP Analogs. ACS Chem Biol 2015; 10:2544-52. [PMID: 26274552 DOI: 10.1021/acschembio.5b00459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleotides containing adenosine play pivotal roles in every living cell. Adenosine triphosphate (ATP), for example, is the universal energy currency, and ATP-consuming processes also contribute to posttranslational protein modifications. Nevertheless, detecting the turnover of adenosine nucleotides in the complex setting of a cell remains challenging. Here, we demonstrate the use of fluorogenic analogs of ATP and adenosine tetraphosphate to study nucleotide hydrolysis in lysates of human cell lines and in intact human cells. We found that the adenosine triphosphate analog is completely stable in lysates of human cell lines, whereas the adenosine tetraphosphate analog is rapidly turned over. The observed activity in human cell lysates can be assigned to a single enzyme, namely, the human diadenosine tetraphosphate hydrolase NudT2. Since NudT2 has been shown to be a prognostic factor for breast cancer, the adenosine tetraphosphate analog might contribute to a better understanding of its involvement in cancerogenesis and allow the straightforward screening for inhibitors. Studying hydrolysis of the analogs in intact cells, we found that electroporation is a suitable method to deliver nucleotide analogs into the cytoplasm and show that high FRET efficiencies can be detected directly after internalization. Time-dependent experiments reveal that adenosine triphosphate and tetraphosphate analogs are both processed in the cellular environment. This study demonstrates that these nucleotide analogs indeed bear the potential to be powerful tools for the exploration of nucleotide turnover in the context of whole cells.
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Affiliation(s)
- Stephan M. Hacker
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Annette Buntz
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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13
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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14
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Hacker SM, Welter M, Marx A. Synthesis of γ-Phosphate-Labeled and Doubly Labeled Adenosine Triphosphate Analogs. ACTA ACUST UNITED AC 2015; 60:13.14.1-13.14.25. [PMID: 25754889 DOI: 10.1002/0471142700.nc1314s60] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit describes the synthesis of γ-phosphate-labeled and doubly labeled adenosine triphosphate (ATP) analogs and their characterization using the phosphodiesterase I from Crotalus adamanteus (snake venom phosphodiesterase; SVPD). In the key step of the synthesis, ATP or an ATP analog, bearing a linker containing a trifluoroacetamide group attached to the nucleoside, are modified with an azide-containing linker at the terminal phosphate using an alkylation reaction. Subsequently, different labels are introduced to the linkers by transformation of one functional group to an amine and coupling to an N-hydroxysuccinimide ester. Specifically, the Staudinger reaction of the azide is employed as a straightforward means to obtain an amine in the presence of various labels. Furthermore, the fluorescence characteristics of a fluorogenic, doubly labeled ATP analog are investigated following enzymatic cleavage by SVPD.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Moritz Welter
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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Gutiérrez Acosta OB, Schleheck D, Schink B. Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins. BMC Genomics 2014; 15:584. [PMID: 25012398 PMCID: PMC4103992 DOI: 10.1186/1471-2164-15-584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. Results In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B12- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone. Conclusions We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-584) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Bernhard Schink
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany.
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