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Li X, Li Z, Zhu J, Wu Z, Dai R, Wang Z. Anaerobic biodegradation enables zero liquid discharge of two-stage nanofiltration system for microelectronic wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134924. [PMID: 38880045 DOI: 10.1016/j.jhazmat.2024.134924] [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: 03/26/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Nanofiltration (NF) is a promising technology in the treatment of microelectronic wastewater. However, the treatment of concentrate derived from NF system remains a substantial technical challenge, impeding the achievement of the zero liquid discharge (ZLD) goal in microelectronic wastewater industries. Herein, a ZLD system, coupling a two-stage NF technology with anaerobic biotechnology was proposed for the treatment of tetramethylammonium hydroxide (TMAH)-contained microelectronic wastewater. The two-stage NF system exhibited favorable efficacy in the removal of conductivity (96 %), total organic carbon (TOC, 90 %), and TMAH (96 %) from microelectronic wastewater. The membrane fouling of this system was dominated by organic fouling, with the second stage NF membrane experiencing a more serious fouling compared to the first stage membrane. The anaerobic biotechnology achieved a near-complete removal of TMAH and an 80 % reduction in TOC for the first stage NF concentrate. Methyloversatilis was the key genus involved in the anaerobic treatment of the microelectronic wastewater concentrate. Specific genes, including dmd-tmd, mtbA, mttB and mttC were identified as significant players in mediating the dehydrogenase and methyl transfer pathways during the process of TMAH biodegradation. This study highlights the potential of anaerobic biodegradation to achieve ZLD in the treatment of TMAH-contained microelectronic wastewater by NF system.
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Affiliation(s)
- Xianfeng Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhouyan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Junhao Zhu
- Green Technology Bank, Shanghai 200082, China
| | - Zhichao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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2
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Wang X, Yu H, Li Y, Fu Q, Shao H, He H, Wang M. Metatranscriptomic insights into the microbial metabolic activities during an Ulva prolifera green tide in coastal Qingdao areas. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123217. [PMID: 38154771 DOI: 10.1016/j.envpol.2023.123217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Green tide, a typical marine environmental disaster that profoundly influenced the coastal areas, has been occurred consecutively in the South Yellow Sea of China since 2007. Herein, the active microbial community structure and metabolic pathways in Qingdao offshore during an Ulva prolifera green tide were investigated by using metatranscriptomic approach. The dominant active microbial taxa at the outbreak phase were primarily a functional group that can utilize organic matters derived from U. prolifera, such as Lentibacter, Polaribacter and Planktomarina. While the taxa involved in biogeochemical cycles, including Phaeobacter, Pseudomonas and Marinobacterium, dominated the active microbial communities at the decline phase. The expression level of enzymes involved in U. prolifera polysaccharides degradation was significantly higher at the outbreak phase compared to the decline phase. At the same time, the main players Glaciecola and Polarbacter showed similar trends, suggesting that the low competitiveness for nutrients of related microorganisms at this phase made them degrade more U. prolifera polysaccharides to meet their own nutrient needs, thereby accelerating the degradation of U. prolifera. According to KEGG annotation, the biogeochemical pathways including nitrogen cycle, sulfur cycle and methane oxidation altered during the green tide, with thiosulfate oxidation and methane oxidation probably being the crucial pathways at the outbreak and the decline phase respectively. The coupling of sulfide oxidation and denitrification was also observed in this study. Furthermore, the green tide in Qingdao offshore might impact the greenhouse effects induced by CH4 and N2O through influencing the related microbial processes.
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Affiliation(s)
- Xinyi Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hao Yu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yan Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Qianru Fu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China.
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Ocean University of China, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao, China
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3
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Magalon A. History of Maturation of Prokaryotic Molybdoenzymes-A Personal View. Molecules 2023; 28:7195. [PMID: 37894674 PMCID: PMC10609526 DOI: 10.3390/molecules28207195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
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Affiliation(s)
- Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
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4
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Zvi-Kedem T, Vintila S, Kleiner M, Tchernov D, Rubin-Blum M. Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels. ISME COMMUNICATIONS 2023; 3:48. [PMID: 37210404 PMCID: PMC10199937 DOI: 10.1038/s43705-023-00254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 04/25/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.
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Affiliation(s)
- Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel.
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5
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Formate hydrogenlyase, formic acid translocation and hydrogen production: dynamic membrane biology during fermentation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148919. [PMID: 36152681 DOI: 10.1016/j.bbabio.2022.148919] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Formate hydrogenlyase-1 (FHL-1) is a complex-I-like enzyme that is commonly found in gram-negative bacteria. The enzyme comprises a peripheral arm and a membrane arm but is not involved in quinone reduction. Instead, FHL-1 couples formate oxidation to the reduction of protons to molecular hydrogen (H2). Escherichia coli produces FHL-1 under fermentative conditions where it serves to detoxify formic acid in the environment. The membrane biology and bioenergetics surrounding E. coli FHL-1 have long held fascination. Here, we review recent work on understanding the molecular basis of formic acid efflux and influx. We also consider the structure and function of E. coli FHL-1, its relationship with formate transport, and pay particular attention to the molecular interface between the peripheral arm and the membrane arm. Finally, we highlight the interesting phenotype of genetic mutation of the ND1 Loop, which is located at that interface.
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6
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Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proc Natl Acad Sci U S A 2022; 119:e2200014119. [PMID: 36067300 PMCID: PMC9477243 DOI: 10.1073/pnas.2200014119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
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7
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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8
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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9
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Masoura M, Milner MT, Overton TW, Gkatzionis K, Lund PA. Use of Transposon Directed Insertion-Site Sequencing to Probe the Antibacterial Mechanism of a Model Honey on E. coli K-12. Front Microbiol 2022; 12:803307. [PMID: 35111142 PMCID: PMC8803141 DOI: 10.3389/fmicb.2021.803307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance is an ever-growing health concern worldwide that has created renewed interest in the use of traditional anti-microbial treatments, including honey. However, understanding the underlying mechanism of the anti-microbial action of honey has been hampered due to the complexity of its composition. High throughput genetic tools could assist in understanding this mechanism. In this study, the anti-bacterial mechanism of a model honey, made of sugars, hydrogen peroxide, and gluconic acid, was investigated using genome-wide transposon mutagenesis combined with high-throughput sequencing (TraDIS), with the strain Escherichia coli K-12 MG1655 as the target organism. We identified a number of genes which when mutated caused a severe loss of fitness when cells were exposed to the model honey. These genes encode membrane proteins including those involved in uptake of essential molecules, and components of the electron transport chain. They are enriched for pathways involved in intracellular homeostasis and redox activity. Genes involved in assembly and activity of formate dehydrogenase O (FDH-O) were of particular note. The phenotypes of mutants in a subset of the genes identified were confirmed by phenotypic screening of deletion strains. We also found some genes which when mutated led to enhanced resistance to treatment with the model honey. This study identifies potential synergies between the main honey stressors and provides insights into the global antibacterial mechanism of this natural product.
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Affiliation(s)
- Maria Masoura
- School of Chemical Engineering, University of Birmingham, Birmingham, United Kingdom
- Institute of Microbiology and Infection (IMI), University of Birmingham, Birmingham, United Kingdom
| | - Mathew T. Milner
- Institute of Microbiology and Infection (IMI), University of Birmingham, Birmingham, United Kingdom
| | - Tim W. Overton
- School of Chemical Engineering, University of Birmingham, Birmingham, United Kingdom
| | - Konstantinos Gkatzionis
- School of Chemical Engineering, University of Birmingham, Birmingham, United Kingdom
- Department of Food Science and Nutrition, School of the Environment, University of the Aegean, Lemnos, Greece
| | - Peter A. Lund
- Institute of Microbiology and Infection (IMI), University of Birmingham, Birmingham, United Kingdom
- *Correspondence: Peter A. Lund,
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10
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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11
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Zhong Q, Kobe B, Kappler U. Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria. Front Microbiol 2020; 11:615860. [PMID: 33362753 PMCID: PMC7759655 DOI: 10.3389/fmicb.2020.615860] [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: 10/10/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.
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Affiliation(s)
- Qifeng Zhong
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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12
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Liu G, Beaton SE, Grieve AG, Evans R, Rogers M, Strisovsky K, Armstrong FA, Freeman M, Exley RM, Tang CM. Bacterial rhomboid proteases mediate quality control of orphan membrane proteins. EMBO J 2020; 39:e102922. [PMID: 32337752 PMCID: PMC7232013 DOI: 10.15252/embj.2019102922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023] Open
Abstract
Although multiprotein membrane complexes play crucial roles in bacterial physiology and virulence, the mechanisms governing their quality control remain incompletely understood. In particular, it is not known how unincorporated, orphan components of protein complexes are recognised and eliminated from membranes. Rhomboids, the most widespread and largest superfamily of intramembrane proteases, are known to play key roles in eukaryotes. In contrast, the function of prokaryotic rhomboids has remained enigmatic. Here, we show that the Shigella sonnei rhomboid proteases GlpG and the newly identified Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes, with the metastable transmembrane domains (TMDs) of rhomboid substrates protected when they are incorporated into a functional complex. Initial cleavage by GlpG or Rhom7 allows subsequent degradation of the orphan substrate. Given the occurrence of this strategy in an evolutionary ancient organism and the presence of rhomboids in all domains of life, it is likely that this form of quality control also mediates critical events in eukaryotes and protects cells from the damaging effects of orphan proteins.
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Affiliation(s)
- Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Stephen E Beaton
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Adam G Grieve
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rhiannon Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Miranda Rogers
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha 6, Czech Republic
| | | | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Leimkühler S. The biosynthesis of the molybdenum cofactors in Escherichia coli. Environ Microbiol 2020; 22:2007-2026. [PMID: 32239579 DOI: 10.1111/1462-2920.15003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5'-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
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Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition. mSystems 2019; 4:4/4/e00280-19. [PMID: 31455638 PMCID: PMC6712303 DOI: 10.1128/msystems.00280-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seagrass-dwelling members of the bivalve family Lucinidae harbor environmentally acquired gill endosymbionts. According to previous studies, lucinid symbionts potentially represent multiple strains from a single thioautotrophic gammaproteobacterium species. This study utilized genomic- and transcriptomic-level data to resolve symbiont taxonomic, genetic, and functional diversity from Ctena orbiculata endosymbiont populations inhabiting carbonate-rich sediment at Sugarloaf Key, FL (USA). The sediment had mixed seagrass and calcareous green alga coverage and also was colonized by at least five other lucinid species. Four coexisting, thioautotrophic endosymbiont operational taxonomic units (OTUs), likely representing four strains from two different bacterial species, were identified from C. orbiculata Three of these OTUs also occurred at high relative abundances in the other sympatric lucinid species. Interspecies genetic differences averaged about 5% lower at both pairwise average nucleotide identity and amino acid identity than interstrain differences. Despite these genetic differences, C. orbiculata endosymbionts shared a high number of metabolic functions, including highly expressed thioautotrophy-related genes and a moderately to weakly expressed conserved one-carbon (C1) oxidation gene cluster previously undescribed in lucinid symbionts. Few symbiont- and host-related genes, including those encoding symbiotic sulfurtransferase, host respiratory functions, and host sulfide oxidation functions, were differentially expressed between seagrass- and alga-covered sediment locations. In contrast to previous studies, the identification of multiple endosymbiont taxa within and across C. orbiculata individuals, which were also shared with other sympatric lucinid species, suggests that neither host nor endosymbiont displays strict taxonomic specificity. This necessitates further investigations into the nature and extent of specificity of lucinid hosts and their symbionts.IMPORTANCE Symbiont diversity and host/symbiont functions have been comprehensively profiled for only a few lucinid species. In this work, unprecedented thioautotrophic gill endosymbiont taxonomic diversity was characterized within a Ctena orbiculata population associated with both seagrass- and alga-covered sediments. Endosymbiont metabolisms included known chemosynthetic functions and an additional conserved, previously uncharacterized C1 oxidation pathway. Lucinid-symbiont associations were not species specific because this C. orbiculata population hosted multiple endosymbiont strains and species, and other sympatric lucinid species shared overlapping symbiont 16S rRNA gene diversity profiles with C. orbiculata Our results suggest that lucinid-symbiont association patterns within some host species could be more taxonomically diverse than previously thought. As such, this study highlights the importance of holistic analyses, at the population, community, and even ecosystem levels, in understanding host-microbe association patterns.
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Bulzu PA, Andrei AŞ, Salcher MM, Mehrshad M, Inoue K, Kandori H, Beja O, Ghai R, Banciu HL. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 2019; 4:1129-1137. [DOI: 10.1038/s41564-019-0404-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/08/2019] [Indexed: 11/09/2022]
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Zupok A, Iobbi-Nivol C, Méjean V, Leimkühler S. The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria. Metallomics 2019; 11:1602-1624. [DOI: 10.1039/c9mt00186g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.
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Affiliation(s)
- Arkadiusz Zupok
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Vincent Méjean
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Silke Leimkühler
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
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Dong G, Ryde U. Reaction mechanism of formate dehydrogenase studied by computational methods. J Biol Inorg Chem 2018; 23:1243-1254. [PMID: 30173398 DOI: 10.1007/s00775-018-1608-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/22/2018] [Indexed: 02/05/2023]
Abstract
Formate dehydrogenases (FDHs) are metalloenzymes that catalyse the reversible conversion of formate to carbon dioxide. Since such a process may be used to combat the greenhouse effect, FDHs have been extensively studied by experimental and theoretical methods. However, the reaction mechanism is still not clear; instead five putative mechanisms have been suggested. In this work, the reaction mechanism of FDH was studied by computational methods. Combined quantum mechanical and molecular mechanic (QM/MM) optimisations were performed to obtain the geometries. To get more accurate energies and obtain a detailed account of the surroundings, big-QM calculations with a very large (1121 atoms) QM region were performed. Our results indicate that the formate substrate does not coordinate directly to Mo when it enters the oxidised active site of the FDH, but instead resides in the second coordination sphere. The sulfido ligand abstracts a hydride ion from the substrate, giving a Mo(IV)-SH state and a thiocarbonate ion attached to Cys196. The latter releases CO2 when the active site is oxidised back to the resting (MoVI) state. This mechanism is supported by recent experimental studies.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00, Lund, Sweden
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 514041, Guangdong, People's Republic of China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00, Lund, Sweden.
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18
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Abstract
Shigella is an intracellular pathogen that invades the human host cell cytosol and exploits intracellular nutrients for growth, enabling the bacterium to create its own metabolic niche. For Shigella to effectively invade and replicate within the host cytoplasm, it must sense and adapt to changing environmental conditions; however, the mechanisms and signals sensed by S. flexneri are largely unknown. We have found that the secreted Shigella metabolism by-product formate regulates Shigella intracellular virulence gene expression and its ability to spread among epithelial cells. We propose that Shigella senses formate accumulation in the host cytosol as a way to determine intracellular Shigella density and regulate secreted virulence factors accordingly, enabling spatiotemporal regulation of effectors important for dampening the host immune response. The intracellular human pathogen Shigella flexneri invades the colon epithelium, replicates to high cell density within the host cell, and then spreads to adjacent epithelial cells. When S. flexneri gains access to the host cytosol, the bacteria metabolize host cytosolic carbon using glycolysis and mixed acid fermentation, producing formate as a by-product. We show that S. flexneri infection results in the accumulation of formate within the host cell. Loss of pyruvate formate lyase (PFL; ΔpflB), which converts pyruvate to acetyl coenzyme A (CoA) and formate, eliminates S. flexneri formate production and reduces the ability of S. flexneri to form plaques in epithelial cell monolayers. This defect in PFL does not decrease the intracellular growth rate of S. flexneri; rather, it affects cell-to-cell spread. The S. flexneri ΔpflB mutant plaque defect is complemented by supplying exogenous formate; conversely, deletion of the S. flexneri formate dehydrogenase gene fdnG increases host cell formate accumulation and S. flexneri plaque size. Furthermore, exogenous formate increases plaque size of the wild-type (WT) S. flexneri strain and promotes S. flexneri cell-to-cell spread. We also demonstrate that formate increases the expression of S. flexneri virulence genes icsA and ipaJ. Intracellular S. flexneriicsA and ipaJ expression is dependent on the presence of formate, and ipaJ expression correlates with S. flexneri intracellular density during infection. Finally, consistent with elevated ipaJ, we show that formate alters S. flexneri-infected host interferon- and tumor necrosis factor (TNF)-stimulated gene expression. We propose that Shigella-derived formate is an intracellular signal that modulates virulence in response to bacterial metabolism.
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Iwadate Y, Funabasama N, Kato JI. Involvement of formate dehydrogenases in stationary phase oxidative stress tolerance in Escherichia coli. FEMS Microbiol Lett 2018; 364:4243112. [PMID: 29044403 DOI: 10.1093/femsle/fnx193] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/11/2017] [Indexed: 01/24/2023] Open
Abstract
Previously, we constructed a series of reduced-genome strains of Escherichia coli by combining large-scale chromosome deletions and then tested the sensitivity of these strains to the redox-cycling drug menadione. In this study, we analyzed a deletion that increased menadione sensitivity and discovered that loss of selenocysteine synthase genes was responsible for the strain's reduced tolerance to oxidative stress. Mutants of formate dehydrogenases, which are selenocysteine-containing enzymes, were also sensitive to menadione, indicating that these enzymes are involved in oxidative stress during stationary phase, specifically under microaerobic conditions in the presence of glucose. Among three formate dehydrogenases encoded by the E. coli genome, two were responsible for the observed phenotypes: formate dehydrogenase-H and -O. In a mutant of fdhD, which encodes a sulfur transferase that is essential for formate dehydrogenase activity, formate dehydrogenase-O could still contribute to oxidative stress tolerance, revealing a novel role for this protein. Consistent with this, overproduction of the electron transfer subunits of this enzyme, FdoH and FdoI, increased menadione tolerance and supported survival in stationary phase. These results suggested that formate dehydrogenase-O serves as an electron transfer element in glucose metabolism to promote oxidative stress tolerance and survival in stationary phase.
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Affiliation(s)
- Yumi Iwadate
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Noriyuki Funabasama
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Jun-Ichi Kato
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
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20
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Hughes ER, Winter MG, Duerkop BA, Spiga L, Furtado de Carvalho T, Zhu W, Gillis CC, Büttner L, Smoot MP, Behrendt CL, Cherry S, Santos RL, Hooper LV, Winter SE. Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis. Cell Host Microbe 2017; 21:208-219. [PMID: 28182951 DOI: 10.1016/j.chom.2017.01.005] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/16/2016] [Accepted: 01/03/2017] [Indexed: 12/16/2022]
Abstract
Intestinal inflammation is frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is characterized by a reduced abundance of obligate anaerobic bacteria and an expansion of facultative Proteobacteria such as commensal E. coli. The mechanisms enabling the outgrowth of Proteobacteria during inflammation are incompletely understood. Metagenomic sequencing revealed bacterial formate oxidation and aerobic respiration to be overrepresented metabolic pathways in a chemically induced murine model of colitis. Dysbiosis was accompanied by increased formate levels in the gut lumen. Formate was of microbial origin since no formate was detected in germ-free mice. Complementary studies using commensal E. coli strains as model organisms indicated that formate dehydrogenase and terminal oxidase genes provided a fitness advantage in murine models of colitis. In vivo, formate served as electron donor in conjunction with oxygen as the terminal electron acceptor. This work identifies bacterial formate oxidation and oxygen respiration as metabolic signatures for inflammation-associated dysbiosis.
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Affiliation(s)
- Elizabeth R Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Breck A Duerkop
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tatiane Furtado de Carvalho
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, 31270 Brazil
| | - Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Caroline C Gillis
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa Büttner
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Madeline P Smoot
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie L Behrendt
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, 31270 Brazil
| | - Lora V Hooper
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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Maia LB, Moura I, Moura JJ. Molybdenum and tungsten-containing formate dehydrogenases: Aiming to inspire a catalyst for carbon dioxide utilization. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.07.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Maia LB, Moura I, Moura JJ. EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Novel Two-Step Hierarchical Screening of Mutant Pools Reveals Mutants under Selection in Chicks. Infect Immun 2016; 84:1226-1238. [PMID: 26857572 DOI: 10.1128/iai.01525-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/02/2016] [Indexed: 11/20/2022] Open
Abstract
Contaminated chicken/egg products are major sources of human salmonellosis, yet the strategies used by Salmonella to colonize chickens are poorly understood. We applied a novel two-step hierarchical procedure to identify new genes important for colonization and persistence of Salmonella enterica serotype Typhimurium in chickens. A library of 182 S. Typhimurium mutants each containing a targeted deletion of a group of contiguous genes (for a total of 2,069 genes deleted) was used to identify regions under selection at 1, 3, and 9 days postinfection in chicks. Mutants in 11 regions were under selection at all assayed times (colonization mutants), and mutants in 15 regions were under selection only at day 9 (persistence mutants). We assembled a pool of 92 mutants, each deleted for a single gene, representing nearly all genes in nine regions under selection. Twelve single gene deletion mutants were under selection in this assay, and we confirmed 6 of 9 of these candidate mutants via competitive infections and complementation analysis in chicks. STM0580, STM1295, STM1297, STM3612, STM3615, and STM3734 are needed for Salmonella to colonize and persist in chicks and were not previously associated with this ability. One of these key genes, STM1297 (selD), is required for anaerobic growth and supports the ability to utilize formate under these conditions, suggesting that metabolism of formate is important during infection. We report a hierarchical screening strategy to interrogate large portions of the genome during infection of animals using pools of mutants of low complexity. Using this strategy, we identified six genes not previously known to be needed during infection in chicks, and one of these (STM1297) suggests an important role for formate metabolism during infection.
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Mienda BS, Shamsir MS, Md. Illias R. Model-assisted formate dehydrogenase-O (fdoH) gene knockout for enhanced succinate production in Escherichia coli from glucose and glycerol carbon sources. J Biomol Struct Dyn 2016; 34:2305-16. [DOI: 10.1080/07391102.2015.1113387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bashir Sajo Mienda
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, Skudai Johor Bahru 81310, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, Skudai Johor Bahru 81310, Malaysia
| | - Rosli Md. Illias
- Faculty of Chemical Engineering, Department of Bioprocess Engineering, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Malaysia
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25
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The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. EcoSal Plus 2015; 6. [PMID: 26442941 DOI: 10.1128/ecosalplus.esp-0005-2013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli contains a versatile respiratory chain that oxidizes 10 different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. Salmonella is able to use two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. A large number of respiratory pathways can be established by combining different electron donors and acceptors. The respiratory dehydrogenases use quinones as the electron acceptors that are oxidized by the terminal reductase and oxidases. The enzymes vary largely with respect to their composition, architecture, membrane topology, and the mode of energy conservation. Most of the energy-conserving dehydrogenases (FdnGHI, HyaABC, HybCOAB, and others) and the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox-loop mechanism. Two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases and terminal reductases do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known or can be predicted. The H+/2e- ratios for most respiratory chains are in the range from 2 to 6 H+/2e-. The energetics of the individual redox reactions and the respiratory chains is described and related to the H+/2e- ratios.
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26
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27
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The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. EcoSal Plus 2015; 3. [PMID: 26443736 DOI: 10.1128/ecosalplus.3.2.2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Escherichia coli contains a versatile respiratory chain which oxidizes ten different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. Salmonella is able to use even two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. Various respiratory pathways can be established by combining the oxidation of different electron donors and acceptors which are linked by respiratory quinones. The enzymes vary largely with respect to architecture, membrane topology, and mode of energy conservation. Most of the energy-conserving dehydrogenases (e.g., FdnGHI, HyaABC, and HybCOAB) and of the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox loop mechanism. Only two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases (e.g., Ndh, SdhABCD, and GlpD) and of terminal reductases (e.g., FrdABCD and DmsABC) do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known from structural and biochemical studies or can be predicted from sequence information. The H+/2e- ratios of proton translocation for most respiratory chains are in the range from 2 to 6 H+/2e-. The energetics of the individual redox reactions and of the respiratory chains is described. In contrast to the knowledge on enzyme function are physiological aspects of respiration such as organization and coordination of the electron transport and the use of alternative respiratory enzymes, not well characterized.
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28
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Hartwig S, Pinske C, Sawers RG. Chromogenic assessment of the three molybdo-selenoprotein formate dehydrogenases in Escherichia coli. Biochem Biophys Rep 2015; 1:62-67. [PMID: 29124134 PMCID: PMC5668559 DOI: 10.1016/j.bbrep.2015.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/05/2015] [Accepted: 03/18/2015] [Indexed: 12/05/2022] Open
Abstract
Escherichia coli synthesizes three selenocysteine-dependent formate dehydrogenases (Fdh) that also have a molybdenum cofactor. Fdh-H couples formate oxidation with proton reduction in the formate hydrogenlyase (FHL) complex. The activity of Fdh-H in solution can be measured with artificial redox dyes but, unlike Fdh-O and Fdh-N, it has never been observed by chromogenic activity staining after non-denaturing polyacrylamide gel electrophoresis (PAGE). Here, we demonstrate that Fdh-H activity is present in extracts of cells from stationary phase cultures and forms a single, fast-migrating species. The activity is oxygen labile during electrophoresis explaining why it has not been previously observed as a discreet activity band. The appearance of Fdh-H activity was dependent on an active selenocysteine incorporation system, but was independent of the [NiFe]-hydrogenases (Hyd), 1, 2 or 3. We also identified new active complexes of Fdh-N and Fdh-O during fermentative growth. The findings of this study indicate that Fdh-H does not form a strong complex with other Fdh or Hyd enzymes, which is in line with it being able to deliver electrons to more than one redox-active enzyme complex. A chromogenic activity stain to identify formate dehydrogenase H was developed. Fdh-H activity was identified in stationary phase fermenting cells. Fdh-H activity was only observed if electrophoresis was performed anaerobically. Fdh-H activity was independent of an active hydrogenase 3 enzyme. New active forms of formate dehydrogenases O and N were identified.
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Affiliation(s)
- Stefanie Hartwig
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Constanze Pinske
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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Hartmann T, Schwanhold N, Leimkühler S. Assembly and catalysis of molybdenum or tungsten-containing formate dehydrogenases from bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1090-100. [PMID: 25514355 DOI: 10.1016/j.bbapap.2014.12.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/04/2014] [Accepted: 12/06/2014] [Indexed: 11/28/2022]
Abstract
The global carbon cycle depends on the biological transformations of C1 compounds, which include the reductive incorporation of CO₂into organic molecules (e.g. in photosynthesis and other autotrophic pathways), in addition to the production of CO₂from formate, a reaction that is catalyzed by formate dehydrogenases (FDHs). FDHs catalyze, in general, the oxidation of formate to CO₂and H⁺. However, selected enzymes were identified to act as CO₂reductases, which are able to reduce CO₂to formate under physiological conditions. This reaction is of interest for the generation of formate as a convenient storage form of H₂for future applications. Cofactor-containing FDHs are found in anaerobic bacteria and archaea, in addition to facultative anaerobic or aerobic bacteria. These enzymes are highly diverse and employ different cofactors such as the molybdenum cofactor (Moco), FeS clusters and flavins, or cytochromes. Some enzymes include tungsten (W) in place of molybdenum (Mo) at the active site. For catalytic activity, a selenocysteine (SeCys) or cysteine (Cys) ligand at the Mo atom in the active site is essential for the reaction. This review will focus on the characterization of Mo- and W-containing FDHs from bacteria, their active site structure, subunit compositions and its proposed catalytic mechanism. We will give an overview on the different mechanisms of substrate conversion available so far, in addition to providing an outlook on bio-applications of FDHs. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Tobias Hartmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany
| | - Nadine Schwanhold
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany.
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Molybdenum and tungsten-dependent formate dehydrogenases. J Biol Inorg Chem 2014; 20:287-309. [DOI: 10.1007/s00775-014-1218-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/09/2014] [Indexed: 11/25/2022]
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Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A. Mapping Cell Envelope and Periplasm Protein Interactions of Escherichia coli Respiratory Formate Dehydrogenases by Chemical Cross-Linking and Mass Spectrometry. J Proteome Res 2014; 13:5524-35. [DOI: 10.1021/pr5004906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Michael Zorn
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | | | | | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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Yokoyama K, Leimkühler S. The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1335-49. [PMID: 25268953 DOI: 10.1016/j.bbamcr.2014.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Metabolic engineering of Escherichia coli to enhance hydrogen production from glycerol. Appl Microbiol Biotechnol 2014; 98:4757-70. [PMID: 24615384 DOI: 10.1007/s00253-014-5600-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022]
Abstract
Glycerol is an attractive carbon source for biofuel production since it is cheap and abundant due to the increasing demand for renewable and clean energy sources, which includes production of biodiesel. This research aims to enhance hydrogen production by Escherichia coli from glycerol by manipulating its metabolic pathways via targeted deletions. Since our past strain, which had been engineered for producing hydrogen from glucose, was not suitable for producing hydrogen from glycerol, we rescreened 14 genes related to hydrogen production and glycerol metabolism. We found that 10 single knockouts are beneficial for enhanced hydrogen production from glycerol, namely, frdC (encoding for furmarate reductase), ldhA (lactate dehydrogenase), fdnG (formate dehydrogenase), ppc (phosphoenolpyruvate carboxylase), narG (nitrate reductase), focA (formate transporter), hyaB (the large subunit of hydrogenase 1), aceE (pyruvate dehydrogenase), mgsA (methylglyoxal synthase), and hycA (a regulator of the transcriptional regulator FhlA). On that basis, we created multiple knockout strains via successive P1 transductions. Simultaneous knockouts of frdC, ldhA, fdnG, ppc, narG, mgsA, and hycA created the best strain that produced 5-fold higher hydrogen and had a 5-fold higher hydrogen yield than the parent strain. The engineered strain also reached the theoretical maximum yield of 1 mol H2/mol glycerol after 48 h. Under low partial pressure fermentation, the strain grew over 2-fold faster, indicating faster utilization of glycerol and production of hydrogen. By combining metabolic engineering and low partial pressure fermentation, hydrogen production from glycerol was enhanced significantly.
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Global identification of genes affecting iron-sulfur cluster biogenesis and iron homeostasis. J Bacteriol 2014; 196:1238-49. [PMID: 24415728 DOI: 10.1128/jb.01160-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors that are crucial for many physiological processes in all organisms. In Escherichia coli, assembly of Fe-S clusters depends on the activity of the iron-sulfur cluster (ISC) assembly and sulfur mobilization (SUF) apparatus. However, the underlying molecular mechanisms and the mechanisms that control Fe-S cluster biogenesis and iron homeostasis are still poorly defined. In this study, we performed a global screen to identify the factors affecting Fe-S cluster biogenesis and iron homeostasis using the Keio collection, which is a library of 3,815 single-gene E. coli knockout mutants. The approach was based on radiolabeling of the cells with [2-(14)C]dihydrouracil, which entirely depends on the activity of an Fe-S enzyme, dihydropyrimidine dehydrogenase. We identified 49 genes affecting Fe-S cluster biogenesis and/or iron homeostasis, including 23 genes important only under microaerobic/anaerobic conditions. This study defines key proteins associated with Fe-S cluster biogenesis and iron homeostasis, which will aid further understanding of the cellular mechanisms that coordinate the processes. In addition, we applied the [2-(14)C]dihydrouracil-labeling method to analyze the role of amino acid residues of an Fe-S cluster assembly scaffold (IscU) as a model of the Fe-S cluster assembly apparatus. The analysis showed that Cys37, Cys63, His105, and Cys106 are essential for the function of IscU in vivo, demonstrating the potential of the method to investigate in vivo function of proteins involved in Fe-S cluster assembly.
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McLean S, Begg R, Jesse HE, Mann BE, Sanguinetti G, Poole RK. Analysis of the bacterial response to Ru(CO)3Cl(Glycinate) (CORM-3) and the inactivated compound identifies the role played by the ruthenium compound and reveals sulfur-containing species as a major target of CORM-3 action. Antioxid Redox Signal 2013; 19:1999-2012. [PMID: 23472713 PMCID: PMC3869425 DOI: 10.1089/ars.2012.5103] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AIMS Carbon monoxide (CO)-releasing molecules (CO-RMs) are being developed with the ultimate goal of safely utilizing the therapeutic potential of CO clinically. One such application is antimicrobial activity; therefore, we aimed to characterize and compare the effects of the CO-RM, CORM-3, and its inactivated counterpart, where all labile CO has been removed, at the transcriptomic and cellular level. RESULTS We found that both compounds are able to penetrate the cell, but the inactive form is not inhibitory to bacterial growth under conditions where CORM-3 is. Transcriptomic analyses revealed that the bacterial response to inactivated CORM-3 (iCORM-3) is much lower than to the active compound and that a wide range of processes appear to be affected by CORM-3 and to a lesser extent iCORM-3, including energy metabolism, membrane transport, motility, and the metabolism of many sulfur-containing species, including cysteine and methionine. INNOVATION This work has demonstrated that both CORM-3 and its inactivated counterpart react with cellular functions to yield a complex response at the transcriptomic level. A full understanding of the actions of both compounds is vital to understand the toxic effects of CO-RMs. CONCLUSION This work has furthered our understanding of how CORM-3 behaves at the cellular level and identifies the responses that occur when the host is exposed to the Ru compound as well as those that result from the released CO. This is a vital step in laying the groundwork for future development of optimized CO-RMs for eventual use in antimicrobial therapy.
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Affiliation(s)
- Samantha McLean
- 1 Department of Molecular Biology and Biotechnology, The University of Sheffield , Sheffield, United Kingdom
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Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A. Selective selC-independent selenocysteine incorporation into formate dehydrogenases. PLoS One 2013; 8:e61913. [PMID: 23634217 PMCID: PMC3636253 DOI: 10.1371/journal.pone.0061913] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/14/2013] [Indexed: 11/18/2022] Open
Abstract
The formate dehydrogenases (Fdh) Fdh-O, Fdh-N, and Fdh-H, are the only proteins in Escherichia coli that incorporate selenocysteine at a specific position by decoding a UGA codon. However, an excess of selenium can lead to toxicity through misincorporation of selenocysteine into proteins. To determine whether selenocysteine substitutes for cysteine, we grew Escherichia coli in the presence of excess sodium selenite. The respiratory Fdh-N and Fdh-O enzymes, along with nitrate reductase (Nar) were co-purified from wild type strain MC4100 after anaerobic growth with nitrate and either 2 µM or 100 µM selenite. Mass spectrometric analysis of the catalytic subunits of both Fdhs identified the UGA-specified selenocysteine residue and revealed incorporation of additional, ‘non-specific’ selenocysteinyl residues, which always replaced particular cysteinyl residues. Although variable, their incorporation was not random and was independent of the selenite concentration used. Notably, these cysteines are likely to be non-essential for catalysis and they do not coordinate the iron-sulfur cluster. The remaining cysteinyl residues that could be identified were never substituted by selenocysteine. Selenomethionine was never observed in our analyses. Non-random substitution of particular cysteinyl residues was also noted in the electron-transferring subunit of both Fdhs as well as in the subunits of the Nar enzyme. Nar isolated from an E. coli selC mutant also showed a similar selenocysteine incorporation pattern to the wild-type indicating that non-specific selenocysteine incorporation was independent of the specific selenocysteine pathway. Thus, selenide replaces sulfide in the biosynthesis of cysteine and misacylated selenocysteyl-tRNACys decodes either UGU or UGC codons, which usually specify cysteine. Nevertheless, not every UGU or UGC codon was decoded as selenocysteine. Together, our results suggest that a degree of misincorporation of selenocysteine into enzymes through replacement of particular, non-essential cysteines, is tolerated and this might act as a buffering system to cope with excessive intracellular selenium.
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Affiliation(s)
- Michael Zorn
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ralph Golbik
- Institute of Biochemistry, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - R. Gary Sawers
- Institute of Microbiology, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (RGS); (AS)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (RGS); (AS)
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38
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Iobbi-Nivol C, Leimkühler S. Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012. [PMID: 23201473 DOI: 10.1016/j.bbabio.2012.11.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molybdenum cofactor (Moco) biosynthesis is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified in bacteria to date. In molybdoenzymes Mo is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into four general steps in bacteria: 1) formation of the cyclic pyranopterin monophosphate, 2) formation of MPT, 3) insertion of molybdenum into molybdopterin to form Moco, and 4) additional modification of Moco with the attachment of GMP or CMP to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on molybdoenzymes, the biosynthesis of Moco, and its incorporation into specific target proteins focusing on Escherichia coli. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Chantal Iobbi-Nivol
- Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Marseille, France
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Westphal K, Langklotz S, Thomanek N, Narberhaus F. A trapping approach reveals novel substrates and physiological functions of the essential protease FtsH in Escherichia coli. J Biol Chem 2012; 287:42962-71. [PMID: 23091052 DOI: 10.1074/jbc.m112.388470] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proteolysis is a universal strategy to rapidly adjust the amount of regulatory and metabolic proteins to cellular demand. FtsH is the only membrane-anchored and essential ATP-dependent protease in Escherichia coli. Among the known functions of FtsH are the control of the heat shock response by proteolysis of the transcription factor RpoH (σ(32)) and its essential role in lipopolysaccharide biosynthesis by degradation of the two key enzymes LpxC and KdtA. Here, we identified new FtsH substrates by using a proteomic-based substrate trapping approach. An FtsH variant (FtsH(trap)) carrying a single amino acid exchange in the proteolytic center was expressed and purified in E. coli. FtsH(trap) is devoid of its proteolytic activity but fully retains ATPase activity allowing for unfolding and translocation of substrates into the inactivated proteolytic chamber. Proteins associated with FtsH(trap) and wild-type FtsH (FtsH(WT)) were purified, separated by two-dimensional PAGE, and subjected to mass spectrometry. Over-representation of LpxC in the FtsH(trap) preparation validated the trapping strategy. Four novel FtsH substrates were identified. The sulfur delivery protein IscS and the d-amino acid dehydrogenase DadA were degraded under all tested conditions. The formate dehydrogenase subunit FdoH and the yet uncharacterized YfgM protein were subject to growth condition-dependent regulated proteolysis. Several lines of evidence suggest that YfgM serves as negative regulator of the RcsB-dependent stress response pathway, which must be degraded under stress conditions. The proteins captured by FtsH(trap) revealed previously unknown biological functions of the physiologically most important AAA(+) protease in E. coli.
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Affiliation(s)
- Kai Westphal
- Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
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40
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Witthoff S, Eggeling L, Bott M, Polen T. Corynebacterium glutamicum harbours a molybdenum cofactor-dependent formate dehydrogenase which alleviates growth inhibition in the presence of formate. Microbiology (Reading) 2012; 158:2428-2439. [DOI: 10.1099/mic.0.059196-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sabrina Witthoff
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Lothar Eggeling
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Michael Bott
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Tino Polen
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
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41
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Heath KD, Burke PV, Stinchcombe JR. Coevolutionary genetic variation in the legume-rhizobium transcriptome. Mol Ecol 2012; 21:4735-47. [PMID: 22672103 DOI: 10.1111/j.1365-294x.2012.05629.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois, 250 Morrill Hall, 505 S. Goodwin Ave., Urbana, IL 61801, USA.
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42
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Babujee L, Apodaca J, Balakrishnan V, Liss P, Kiley PJ, Charkowski AO, Glasner JD, Perna NT. Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria. BMC Genomics 2012; 13:110. [PMID: 22439737 PMCID: PMC3349551 DOI: 10.1186/1471-2164-13-110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 03/22/2012] [Indexed: 01/31/2023] Open
Abstract
Background Dickeya dadantii and Pectobacterium atrosepticum are phytopathogenic enterobacteria capable of facultative anaerobic growth in a wide range of O2 concentrations found in plant and natural environments. The transcriptional response to O2 remains under-explored for these and other phytopathogenic enterobacteria although it has been well characterized for animal-associated genera including Escherichia coli and Salmonella enterica. Knowledge of the extent of conservation of the transcriptional response across orthologous genes in more distantly related species is useful to identify rates and patterns of regulon evolution. Evolutionary events such as loss and acquisition of genes by lateral transfer events along each evolutionary branch results in lineage-specific genes, some of which may have been subsequently incorporated into the O2-responsive stimulon. Here we present a comparison of transcriptional profiles measured using densely tiled oligonucleotide arrays for two phytopathogens, Dickeya dadantii 3937 and Pectobacterium atrosepticum SCRI1043, grown to mid-log phase in MOPS minimal medium (0.1% glucose) with and without O2. Results More than 7% of the genes of each phytopathogen are differentially expressed with greater than 3-fold changes under anaerobic conditions. In addition to anaerobic metabolism genes, the O2 responsive stimulon includes a variety of virulence and pathogenicity-genes. Few of these genes overlap with orthologous genes in the anaerobic stimulon of E. coli. We define these as the conserved core, in which the transcriptional pattern as well as genetic architecture are well preserved. This conserved core includes previously described anaerobic metabolic pathways such as fermentation. Other components of the anaerobic stimulon show variation in genetic content, genome architecture and regulation. Notably formate metabolism, nitrate/nitrite metabolism, and fermentative butanediol production, differ between E. coli and the phytopathogens. Surprisingly, the overlap of the anaerobic stimulon between the phytopathogens is also relatively small considering that they are closely related, occupy similar niches and employ similar strategies to cause disease. There are cases of interesting divergences in the pattern of transcription of genes between Dickeya and Pectobacterium for virulence-associated subsystems including the type VI secretion system (T6SS), suggesting that fine-tuning of the stimulon impacts interaction with plants or competing microbes. Conclusions The small number of genes (an even smaller number if we consider operons) comprising the conserved core transcriptional response to O2 limitation demonstrates the extent of regulatory divergence prevalent in the Enterobacteriaceae. Our orthology-driven comparative transcriptomics approach indicates that the adaptive response in the eneterobacteria is a result of interaction of core (regulators) and lineage-specific (structural and regulatory) genes. Our subsystems based approach reveals that similar phenotypic outcomes are sometimes achieved by each organism using different genes and regulatory strategies.
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Affiliation(s)
- Lavanya Babujee
- Biotechnology Center, University of Wisconsin-Madison, WI, USA
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Pinske C, Sawers RG. A-type carrier protein ErpA is essential for formation of an active formate-nitrate respiratory pathway in Escherichia coli K-12. J Bacteriol 2012; 194:346-53. [PMID: 22081393 PMCID: PMC3256641 DOI: 10.1128/jb.06024-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/01/2011] [Indexed: 02/04/2023] Open
Abstract
A-type carrier (ATC) proteins of the Isc (iron-sulfur cluster) and Suf (sulfur mobilization) iron-sulfur ([Fe-S]) cluster biogenesis pathways are proposed to traffic preformed [Fe-S] clusters to apoprotein targets. In this study, we analyzed the roles of the ATC proteins ErpA, IscA, and SufA in the maturation of the nitrate-inducible, multisubunit anaerobic respiratory enzymes formate dehydrogenase N (Fdh-N) and nitrate reductase (Nar). Mutants lacking SufA had enhanced activities of both enzymes. While both Fdh-N and Nar activities were strongly reduced in an iscA mutant, both enzymes were inactive in an erpA mutant and in a mutant unable to synthesize the [Fe-S] cluster scaffold protein IscU. It could be shown for both Fdh-N and Nar that loss of enzyme activity correlated with absence of the [Fe-S] cluster-containing small subunit. Moreover, a slowly migrating form of the catalytic subunit FdnG of Fdh-N was observed, consistent with impeded twin arginine translocation (TAT)-dependent transport. The highly related Fdh-O enzyme was also inactive in the erpA mutant. Although the Nar enzyme has its catalytic subunit NarG localized in the cytoplasm, it also exhibited aberrant migration in an erpA iscA mutant, suggesting that these modular enzymes lack catalytic integrity due to impaired cofactor biosynthesis. Cross-complementation experiments demonstrated that multicopy IscA could partially compensate for lack of ErpA with respect to Fdh-N activity but not Nar activity. These findings suggest that ErpA and IscA have overlapping roles in assembly of these anaerobic respiratory enzymes but demonstrate that ErpA is essential for the production of active enzymes.
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Affiliation(s)
- Constanze Pinske
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Thomé R, Gust A, Toci R, Mendel R, Bittner F, Magalon A, Walburger A. A sulfurtransferase is essential for activity of formate dehydrogenases in Escherichia coli. J Biol Chem 2011; 287:4671-8. [PMID: 22194618 DOI: 10.1074/jbc.m111.327122] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
l-Cysteine desulfurases provide sulfur to several metabolic pathways in the form of persulfides on specific cysteine residues of an acceptor protein for the eventual incorporation of sulfur into an end product. IscS is one of the three Escherichia coli l-cysteine desulfurases. It interacts with FdhD, a protein essential for the activity of formate dehydrogenases (FDHs), which are iron/molybdenum/selenium-containing enzymes. Here, we address the role played by this interaction in the activity of FDH-H (FdhF) in E. coli. The interaction of IscS with FdhD results in a sulfur transfer between IscS and FdhD in the form of persulfides. Substitution of the strictly conserved residue Cys-121 of FdhD impairs both sulfur transfer from IscS to FdhD and FdhF activity. Furthermore, inactive FdhF produced in the absence of FdhD contains both metal centers, albeit the molybdenum cofactor is at a reduced level. Finally, FdhF activity is sulfur-dependent, as it shows reversible sensitivity to cyanide treatment. Conclusively, FdhD is a sulfurtransferase between IscS and FdhF and is thereby essential to yield FDH activity.
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Affiliation(s)
- Rémi Thomé
- Laboratoire de Chimie Bactérienne, UPR9043, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, 13009 Marseille, France
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45
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Pinske C, Bönn M, Krüger S, Lindenstrauß U, Sawers RG. Metabolic deficiences revealed in the biotechnologically important model bacterium Escherichia coli BL21(DE3). PLoS One 2011; 6:e22830. [PMID: 21826210 PMCID: PMC3149613 DOI: 10.1371/journal.pone.0022830] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/01/2011] [Indexed: 11/26/2022] Open
Abstract
The Escherichia coli B strain BL21(DE3) has had a profound impact on biotechnology through its use in the production of recombinant proteins. Little is understood, however, regarding the physiology of this important E. coli strain. We show here that BL21(DE3) totally lacks activity of the four [NiFe]-hydrogenases, the three molybdenum- and selenium-containing formate dehydrogenases and molybdenum-dependent nitrate reductase. Nevertheless, all of the structural genes necessary for the synthesis of the respective anaerobic metalloenzymes are present in the genome. However, the genes encoding the high-affinity molybdate transport system and the molybdenum-responsive transcriptional regulator ModE are absent from the genome. Moreover, BL21(DE3) has a nonsense mutation in the gene encoding the global oxygen-responsive transcriptional regulator FNR. The activities of the two hydrogen-oxidizing hydrogenases, therefore, could be restored to BL21(DE3) by supplementing the growth medium with high concentrations of Ni²⁺ (Ni²⁺-transport is FNR-dependent) or by introducing a wild-type copy of the fnr gene. Only combined addition of plasmid-encoded fnr and high concentrations of MoO₄²⁻ ions could restore hydrogen production to BL21(DE3); however, to only 25-30% of a K-12 wildtype. We could show that limited hydrogen production from the enzyme complex responsible for formate-dependent hydrogen evolution was due solely to reduced activity of the formate dehydrogenase (FDH-H), not the hydrogenase component. The activity of the FNR-dependent formate dehydrogenase, FDH-N, could not be restored, even when the fnr gene and MoO₄²⁻ were supplied; however, nitrate reductase activity could be recovered by combined addition of MoO₄²⁻ and the fnr gene. This suggested that a further component specific for biosynthesis or activity of formate dehydrogenases H and N was missing. Re-introduction of the gene encoding ModE could only partially restore the activities of both enzymes. Taken together these results demonstrate that BL21(DE3) has major defects in anaerobic metabolism, metal ion transport and metalloprotein biosynthesis.
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Affiliation(s)
- Constanze Pinske
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Markus Bönn
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sara Krüger
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ute Lindenstrauß
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R. Gary Sawers
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Soboh B, Pinske C, Kuhns M, Waclawek M, Ihling C, Trchounian K, Trchounian A, Sinz A, Sawers G. The respiratory molybdo-selenoprotein formate dehydrogenases of Escherichia coli have hydrogen: benzyl viologen oxidoreductase activity. BMC Microbiol 2011; 11:173. [PMID: 21806784 PMCID: PMC3160892 DOI: 10.1186/1471-2180-11-173] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 08/01/2011] [Indexed: 11/25/2022] Open
Abstract
Background Escherichia coli synthesizes three membrane-bound molybdenum- and selenocysteine-containing formate dehydrogenases, as well as up to four membrane-bound [NiFe]-hydrogenases. Two of the formate dehydrogenases (Fdh-N and Fdh-O) and two of the hydrogenases (Hyd-1 and Hyd-2) have their respective catalytic subunits located in the periplasm and these enzymes have been shown previously to oxidize formate and hydrogen, respectively, and thus function in energy metabolism. Mutants unable to synthesize the [NiFe]-hydrogenases retain a H2: benzyl viologen oxidoreductase activity. The aim of this study was to identify the enzyme or enzymes responsible for this activity. Results Here we report the identification of a new H2: benzyl viologen oxidoreductase enzyme activity in E. coli that is independent of the [NiFe]-hydrogenases. This enzyme activity was originally identified after non-denaturing polyacrylamide gel electrophoresis and visualization of hydrogen-oxidizing activity by specific staining. Analysis of a crude extract derived from a variety of E. coli mutants unable to synthesize any [NiFe]-hydrogenase-associated enzyme activity revealed that the mutants retained this specific hydrogen-oxidizing activity. Enrichment of this enzyme activity from solubilised membrane fractions of the hydrogenase-negative mutant FTD147 by ion-exchange, hydrophobic interaction and size-exclusion chromatographies followed by mass spectrometric analysis identified the enzymes Fdh-N and Fdh-O. Analysis of defined mutants devoid of selenocysteine biosynthetic capacity or carrying deletions in the genes encoding the catalytic subunits of Fdh-N and Fdh-O demonstrated that both enzymes catalyze hydrogen activation. Fdh-N and Fdh-O can also transfer the electrons derived from oxidation of hydrogen to other redox dyes. Conclusions The related respiratory molybdo-selenoproteins Fdh-N and Fdh-O of Escherichia coli have hydrogen-oxidizing activity. These findings demonstrate that the energy-conserving selenium- and molybdenum-dependent formate dehydrogenases Fdh-N and Fdh-O exhibit a degree of promiscuity with respect to the electron donor they use and identify a new class of dihydrogen-oxidizing enzyme.
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Affiliation(s)
- Basem Soboh
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str, 3, 06120 Halle (Saale), Germany
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47
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Crable BR, Plugge CM, McInerney MJ, Stams AJM. Formate formation and formate conversion in biological fuels production. Enzyme Res 2011; 2011:532536. [PMID: 21687599 PMCID: PMC3112519 DOI: 10.4061/2011/532536] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 03/23/2011] [Indexed: 11/20/2022] Open
Abstract
Biomethanation is a mature technology for fuel production. Fourth generation biofuels research will focus on sequestering CO(2) and providing carbon-neutral or carbon-negative strategies to cope with dwindling fossil fuel supplies and environmental impact. Formate is an important intermediate in the methanogenic breakdown of complex organic material and serves as an important precursor for biological fuels production in the form of methane, hydrogen, and potentially methanol. Formate is produced by either CoA-dependent cleavage of pyruvate or enzymatic reduction of CO(2) in an NADH- or ferredoxin-dependent manner. Formate is consumed through oxidation to CO(2) and H(2) or can be further reduced via the Wood-Ljungdahl pathway for carbon fixation or industrially for the production of methanol. Here, we review the enzymes involved in the interconversion of formate and discuss potential applications for biofuels production.
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Affiliation(s)
- Bryan R Crable
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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48
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Abstract
Hydrogen fuel is renewable, efficient and clean, and fermentative bacteria hold great promise for its generation. Here we use the isogenic Escherichia coli K‐12 KEIO library to rapidly construct multiple, precise deletions in the E. coli genome to direct the metabolic flux towards hydrogen production. Escherichia coli has three active hydrogenases, and the genes involved in the regulation of the formate hydrogen lyase (FHL) system for synthesizing hydrogen from formate via hydrogenase 3 were also manipulated to enhance hydrogen production. Specifically, we altered regulation of FHL by controlling the regulators HycA and FhlA, removed hydrogen consumption by hydrogenases 1 and 2 via the hyaB and hybC mutations, and re‐directed formate metabolism using the fdnG, fdoG, narG, focA, fnr and focB mutations. The result was a 141‐fold increase in hydrogen production from formate to create a bacterium (BW25113 hyaB hybC hycA fdoG/pCA24N‐FhlA) that produces the largest amount of hydrogen to date and one that achieves the theoretical yield for hydrogen from formate. In addition, the hydrogen yield from glucose was increased by 50%, and there was threefold higher hydrogen production from glucose with this strain.
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Affiliation(s)
- Toshinari Maeda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
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49
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Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky TS. Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res 2010; 38:5893-908. [PMID: 20460466 PMCID: PMC2943607 DOI: 10.1093/nar/gkq281] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We experimentally identified and characterized 97 novel, non-protein-coding RNA candidates (npcRNAs) from the human pathogen Salmonella enterica serovar Typhi (hereafter referred to as S. typhi). Three were specific to S. typhi, 22 were restricted to Salmonella species and 33 were differentially expressed during S. typhi growth. We also identified Salmonella Pathogenicity Island-derived npcRNAs that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of S. typhi. An in-depth characterization of S. typhi StyR-3 npcRNA showed that it specifically interacts with RamR, the transcriptional repressor of the ramA gene, which is involved in the multidrug resistance (MDR) of Salmonella. StyR-3 interfered with RamR–DNA binding activity and thus potentially plays a role in regulating ramA gene expression, resulting in the MDR phenotype. Our study also revealed a large number of cis-encoded antisense npcRNA candidates, supporting previous observations of global sense–antisense regulatory networks in bacteria. Finally, at least six of the npcRNA candidates interacted with the S. typhi Hfq protein, supporting an important role of Hfq in npcRNA networks. This study points to novel functional npcRNA candidates potentially involved in various regulatory roles including the pathogenicity of S. typhi.
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Affiliation(s)
- Suresh V Chinni
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
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50
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Dalai B, Zhou R, Wan Y, Kang M, Li L, Li T, Zhang S, Chen H. Histone-like protein H-NS regulates biofilm formation and virulence of Actinobacillus pleuropneumoniae. Microb Pathog 2008; 46:128-34. [PMID: 19095055 DOI: 10.1016/j.micpath.2008.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2008] [Revised: 11/18/2008] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
Abstract
Actinobacillus pleuropneumoniae is the causative agent of porcine contagious pleuropneumonia, a very important swine respiratory infectious disease causing great economic losses worldwide. The pathogenesis of this disease is still not completely understood. Biofilm formation contributes to full virulence in many Gram-negative bacterial pathogens. In the present study, two biofilm-producing mutants were identified from the transposon mutagenesis mutant pools of A. pleuropneumoniae strain 4074 of serovar 1 (a non-biofilm forming strain). Inverse PCR and sequencing analysis revealed that the hns gene encoding the histone-like nucleoid structuring protein (H-NS) was inactivated by the mini-Tn10 transposon in both mutant strains. Further analysis revealed that the virulence was attenuated in the mutant strains when their haemolytic activity and 50% lethal doses in mice were compared with the parental strain. Real-time RT-PCR analysis suggested that the down-regulation of the exotoxin genes in the hns mutants may partly contribute to the virulence attenuation. Our data indicate that H-NS plays important roles in regulating biofilm formation and virulence in A. pleuropneumoniae.
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Affiliation(s)
- Baolige Dalai
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Shizishan Street 1, Wuhan 430070, China
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