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Liu H, Liu T, Chen S, Liu X, Li N, Huang T, Ma B, Liu X, Pan S, Zhang H. Biogeochemical cycles of iron: Processes, mechanisms, and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175722. [PMID: 39187081 DOI: 10.1016/j.scitotenv.2024.175722] [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: 07/02/2024] [Revised: 07/29/2024] [Accepted: 08/08/2024] [Indexed: 08/28/2024]
Abstract
The iron (Fe) biogeochemical cycle is critical for abiotic and biological environmental processes that overlap spatially and may compete with each other. The development of modern molecular biology technologies promoted the understanding of the electron transport mechanisms of Fe-cycling-related microorganisms. Recent studies have revealed a novel pathway for microaerophilic ferrous iron (Fe(II))-oxidizers in extracellular Fe(II) oxidation. In addition, OmcS, OmcZ, and OmcE nanowires on the cell surface have been shown to promote electron transfer between microorganisms and their environment. These processes affect the fate of pollutants in directly or indirectly ways, such as greenhouse gas emissions. In this review, these advances and the environmental implications of the Fe cycle process were discussed, with a particular focus on the mechanisms of intracellular or extracellular electron transport in microorganisms.
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Affiliation(s)
- Huan Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tao Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Shengnan Chen
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiaoyan Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Nan Li
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Tinglin Huang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiang Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Sixuan Pan
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Haihan Zhang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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Li S, Wang J, Liu J, Zhang H, Bao T, Sun C, Fang J, Cao J. Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation. Microorganisms 2023; 11:microorganisms11030798. [PMID: 36985371 PMCID: PMC10059138 DOI: 10.3390/microorganisms11030798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/27/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the Mariana Trench at a depth of 5900 m. Here, we report its complete genome sequence and adaptation strategies for survival in deep-sea environments. MTB7 contains what is currently the third-largest genome among all isolated Shewanella strains and shows higher coding density than neighboring strains. Metabolically, MTB7 is predicted to utilize various carbon and nitrogen sources. D-amino acid utilization and HGT-derived purine-degrading genes could contribute to its oligotrophic adaptation. For respiration, the cytochrome o ubiquinol oxidase genes cyoABCDE, typically expressed at high oxygen concentrations, are missing. Conversely, a series of anaerobic respiratory genes are employed, including fumarate reductase, polysulfide reductase, trimethylamine-N-oxide reductase, crotonobetaine reductase, and Mtr subunits. The glycine reductase genes and the triplication of dimethyl sulfoxide reductase genes absent in neighboring strains could also help MTB7 survive in low-oxygen environments. Many genes encoding cold-shock proteins, glycine betaine transporters and biosynthetic enzymes, and reactive oxygen species-scavenging proteins could contribute to its low-temperature adaptation. The genomic analysis of MTB7 will deepen our understanding of microbial adaptation strategies in deep-sea environments.
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Affiliation(s)
- Sicong Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jie Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Hongcai Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Tianqiang Bao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Chengwen Sun
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
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Zhang D, Ke T, Xiu W, Ren C, Chen G, Lloyd JR, Bassil NM, Richards LA, Polya DA, Wang G, Guo H. Quantifying sulfidization and non-sulfidization in long-term in-situ microbial colonized As(V)-ferrihydrite coated sand columns: Insights into As mobility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160066. [PMID: 36356776 DOI: 10.1016/j.scitotenv.2022.160066] [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: 06/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Sulfide-induced reduction (sulfidization) of arsenic (As)-bearing Fe(III) (oxyhydro)oxides may lead to As mobilization in aquifer systems. However, little is known about the relative contributions of sulfidization and non-sulfidization of Fe(III) (oxyhydro)oxides reduction to As mobilization. To address this issue, high As groundwater with low sulfide (LS) and high sulfide (HS) concentrations were pumped through As(V)-bearing ferrihydrite-coated sand columns (LS-column and HS-column, respectively) being settled within wells in the western Hetao Basin, China. Sulfidization of As(V)-bearing ferrihydrite was evidenced by the increase in dissolved Fe(II) and the presence of solid Fe(II) and elemental sulfur (S0) in both the columns. A conceptual model was built using accumulated S0 and Fe(II) produced in the columns to calculate the proportions of sulfidization-induced Fe(III) (oxyhydro)oxide reduction and non-sulfidization-induced Fe(III) (oxyhydro)oxide reduction. Fe(III) reduction via sulfidization occurred preferentially in the inlet ends (LS-column, 31 %; HS-column, 86 %), while Fe(III) reduction via non-sulfidization processes predominated in the outlet ends (LS-column, 96 %; HS-column, 86 %), and was attributed to the metabolism of genera associated with Fe(III) reduction (including Shewanella, Ferribacterium, and Desulfuromonas). Arsenic was mobilized in the columns via sulfidization and non-sulfidization processes. More As was released from the solid of the HS-column than that of the LS-column due to the higher intensity of sulfidization in the presence of higher concentrations of dissolved S(-II). Overall, this study highlights the sulfidization of As-bearing Fe(III) (oxyhydro)oxides as an important As-mobilizing pathway in complex As-Fe-S bio-hydrogeochemical networks.
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Affiliation(s)
- Di Zhang
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Tiantian Ke
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China; Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom.
| | - Cui Ren
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Guangyu Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Naji M Bassil
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Laura A Richards
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - David A Polya
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China.
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Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt. Microorganisms 2022; 10:microorganisms10081585. [PMID: 36014003 PMCID: PMC9415397 DOI: 10.3390/microorganisms10081585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.
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Kawabata T. Iron-Induced Oxidative Stress in Human Diseases. Cells 2022; 11:cells11142152. [PMID: 35883594 PMCID: PMC9324531 DOI: 10.3390/cells11142152] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Iron is responsible for the regulation of several cell functions. However, iron ions are catalytic and dangerous for cells, so the cells sequester such redox-active irons in the transport and storage proteins. In systemic iron overload and local pathological conditions, redox-active iron increases in the human body and induces oxidative stress through the formation of reactive oxygen species. Non-transferrin bound iron is a candidate for the redox-active iron in extracellular space. Cells take iron by the uptake machinery such as transferrin receptor and divalent metal transporter 1. These irons are delivered to places where they are needed by poly(rC)-binding proteins 1/2 and excess irons are stored in ferritin or released out of the cell by ferroportin 1. We can imagine transit iron pool in the cell from iron import to the export. Since the iron in the transit pool is another candidate for the redox-active iron, the size of the pool may be kept minimally. When a large amount of iron enters cells and overflows the capacity of iron binding proteins, the iron behaves as a redox-active iron in the cell. This review focuses on redox-active iron in extracellular and intracellular spaces through a biophysical and chemical point of view.
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Affiliation(s)
- Teruyuki Kawabata
- Department of Applied Physics, Postgraduate School of Science, Okayama University of Science, Okayama 700-0005, Japan
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Okazaki Y. The Role of Ferric Nitrilotriacetate in Renal Carcinogenesis and Cell Death: From Animal Models to Clinical Implications. Cancers (Basel) 2022; 14:cancers14061495. [PMID: 35326646 PMCID: PMC8946552 DOI: 10.3390/cancers14061495] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 12/17/2022] Open
Abstract
Iron is essential for cellular growth, and various ferroproteins and heme-containing proteins are involved in a myriad of cellular functions, such as DNA synthesis, oxygen transport, and catalytic reactions. As a consequence, iron deficiency causes pleiotropic effects, such as hypochromic microcytic anemia and growth disturbance, while iron overload is also deleterious by oxidative injury. To prevent the generation of iron-mediated reactive oxygen species (ROS), ferritin is synthesized to store excess iron in cells that are consistent with the clinical utility of the serum ferritin concentration to monitor the therapeutic effect of iron-chelation. Among the animal models exploring iron-induced oxidative stress, ferric nitrilotriacetate (Fe-NTA) was shown to initiate hepatic and renal lipid peroxidation and the development of renal cell carcinoma (RCC) after repeated intraperitoneal injections of Fe-NTA. Here, current understanding of Fe-NTA-induced oxidative stress mediated by glutathione-cycle-dependent iron reduction and the molecular mechanisms of renal carcinogenesis are summarized in combination with a summary of the relationship between the pathogenesis of human RCC and iron metabolism. In addition to iron-mediated carcinogenesis, the ferroptosis that is triggered by the iron-dependent accumulation of lipid peroxidation and is implicated in the carcinogenesis is discussed.
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Affiliation(s)
- Yasumasa Okazaki
- Department of Pathology and Biological Responses, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-Ku, Nagoya 466-8550, Japan
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Werwinski S, Wharton JA, Nie M, Stokes KR. Electrochemical Sensing and Characterization of Aerobic Marine Bacterial Biofilms on Gold Electrode Surfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:31393-31405. [PMID: 34184862 DOI: 10.1021/acsami.1c02669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Reliable and accurate in situ sensors capable of detecting and quantifying troublesome marine biofilms on metallic surfaces are increasingly necessary. A 0.2 mm diameter gold electrochemical sensor was fully characterized using cyclic voltammetry in abiotic and biotic artificial seawater media within a continuous culture flow cell to detect the growth and development of an aerobic Pseudoalteromonas sp. biofilm. Deconvolution of the abiotic and biotic responses enable the constituent extracellular electron transfer and biofilm responses to be resolved. Differentiation of enhanced oxygen reduction kinetics within the aerobic bacterial biofilm is linked to enzyme and redox mediator activities.
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Affiliation(s)
- Stephane Werwinski
- National Centre for Advanced Tribology at Southampton (nCATS), School of Engineering, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Julian A Wharton
- National Centre for Advanced Tribology at Southampton (nCATS), School of Engineering, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Mengyan Nie
- UCL Institute for Materials Discovery, University College London, Malet Place, London WC1E 7JE, U.K
| | - Keith R Stokes
- National Centre for Advanced Tribology at Southampton (nCATS), School of Engineering, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
- Physical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, U.K
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Huang J, Jones A, Waite TD, Chen Y, Huang X, Rosso KM, Kappler A, Mansor M, Tratnyek PG, Zhang H. Fe(II) Redox Chemistry in the Environment. Chem Rev 2021; 121:8161-8233. [PMID: 34143612 DOI: 10.1021/acs.chemrev.0c01286] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Iron (Fe) is the fourth most abundant element in the earth's crust and plays important roles in both biological and chemical processes. The redox reactivity of various Fe(II) forms has gained increasing attention over recent decades in the areas of (bio) geochemistry, environmental chemistry and engineering, and material sciences. The goal of this paper is to review these recent advances and the current state of knowledge of Fe(II) redox chemistry in the environment. Specifically, this comprehensive review focuses on the redox reactivity of four types of Fe(II) species including aqueous Fe(II), Fe(II) complexed with ligands, minerals bearing structural Fe(II), and sorbed Fe(II) on mineral oxide surfaces. The formation pathways, factors governing the reactivity, insights into potential mechanisms, reactivity comparison, and characterization techniques are discussed with reference to the most recent breakthroughs in this field where possible. We also cover the roles of these Fe(II) species in environmental applications of zerovalent iron, microbial processes, biogeochemical cycling of carbon and nutrients, and their abiotic oxidation related processes in natural and engineered systems.
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Affiliation(s)
- Jianzhi Huang
- Department of Civil and Environmental Engineering, Case Western Reserve University, 2104 Adelbert Road, Cleveland, Ohio 44106, United States
| | - Adele Jones
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - T David Waite
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaopeng Huang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kevin M Rosso
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, 72076 Tuebingen, Germany
| | - Muammar Mansor
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, 72076 Tuebingen, Germany
| | - Paul G Tratnyek
- School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Huichun Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, 2104 Adelbert Road, Cleveland, Ohio 44106, United States
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Kappler A, Bryce C, Mansor M, Lueder U, Byrne JM, Swanner ED. An evolving view on biogeochemical cycling of iron. Nat Rev Microbiol 2021; 19:360-374. [PMID: 33526911 DOI: 10.1038/s41579-020-00502-7] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2020] [Indexed: 01/23/2023]
Abstract
Biogeochemical cycling of iron is crucial to many environmental processes, such as ocean productivity, carbon storage, greenhouse gas emissions and the fate of nutrients, toxic metals and metalloids. Knowledge of the underlying processes involved in iron cycling has accelerated in recent years along with appreciation of the complex network of biotic and abiotic reactions dictating the speciation, mobility and reactivity of iron in the environment. Recent studies have provided insights into novel processes in the biogeochemical iron cycle such as microbial ammonium oxidation and methane oxidation coupled to Fe(III) reduction. They have also revealed that processes in the biogeochemical iron cycle spatially overlap and may compete with each other, and that oxidation and reduction of iron occur cyclically or simultaneously in many environments. This Review discusses these advances with particular focus on their environmental consequences, including the formation of greenhouse gases and the fate of nutrients and contaminants.
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Affiliation(s)
- Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany.
| | - Casey Bryce
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Muammar Mansor
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Ulf Lueder
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - James M Byrne
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Elizabeth D Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, USA
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Lokesh S, Kim J, Zhou Y, Wu D, Pan B, Wang X, Behrens S, Huang CH, Yang Y. Anaerobic Dehalogenation by Reduced Aqueous Biochars. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15142-15150. [PMID: 33170651 DOI: 10.1021/acs.est.0c05940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dehalogenation is one of the most important reactions for eliminating trace organic pollutants in natural and engineering systems. This study investigated the dehalogenation of a model organohalogen compound, triclosan (TCS), by aqueous biochars (a-BCs) (<450 nm). We found that TCS can be anaerobically degraded by reduced a-BCs with a pseudo first-order degradation rate constant of 0.0011-0.011 h-1. The 288 h degradation fraction of TCS correlated significantly with the amount of a-BC-bound electrons (0.055 ± 0.00024 to 0.11 ± 0.0016 mol e-/mol C) available for donation after 24 h of pre-reduction by Shewanella putrefaciens CN32. Within the reduction period, the recovery of chlorine based on residual TCS and generated Cl- ranged from 73.6 to 85.2%, implying that a major fraction of TCS was fully dechlorinated, together with mass spectroscopic analysis of possible degradation byproducts. Least-squares numerical fitting, accounting for the reactions of hydroquinones/semiquinones in a-BCs with TCS and byproducts, can simulate the reaction kinetics well (R2 > 0.76) and suggest the first-step dechlorination as the rate-limiting step among the possible pathways. These results showcased that the reduced a-BCs can reductively degrade organohalogens with potential applications for wastewater treatment and groundwater remediation. While TCS was used as a model compound in this study, a-BC-based degradation can be likely applied to a range of redox-sensitive trace organic compounds.
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Affiliation(s)
- Srinidhi Lokesh
- Department of Civil and Environmental Engineering, University of Nevada, Reno, Nevada 89557-0258, United States
| | - Juhee Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Yuwei Zhou
- Department of Civil and Environmental Engineering, University of Nevada, Reno, Nevada 89557-0258, United States
| | - Danping Wu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Bo Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Xilong Wang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, P.R. China
| | - Sebastian Behrens
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, Minnesota 55455-0116, United States
| | - Ching-Hua Huang
- Department of Civil and Environmental Engineering, University of Nevada, Reno, Nevada 89557-0258, United States
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada, Reno, Nevada 89557-0258, United States
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Sun X, Qiu L, Kolton M, Häggblom M, Xu R, Kong T, Gao P, Li B, Jiang C, Sun W. V V Reduction by Polaromonas spp. in Vanadium Mine Tailings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14442-14454. [PMID: 33125214 DOI: 10.1021/acs.est.0c05328] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Vanadium (V) is an important metal with critical industrial and medical applications. Elevated V contamination, however, can be a threat to the environment and human health. Microorganisms can reduce the more toxic and mobile VV to the less toxic and immobile VIV, which could be a detoxification and energy metabolism strategy adopted by V-reducing bacteria (VRB). The limited understanding of microbial responses to V contamination and the mechanisms for VV reduction, however, hamper our capability to attenuate V contamination. This study focused on determining the microbial responses to elevated V concentration and the mechanisms of VV reduction in V tailings. The bacterial communities were characterized and compared between the V tailings and the less contaminated adjacent mineral soils. Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction. Retrieved metagenome-assembled genomes (MAGs) suggested that the Polaromonas spp. encoded genes (cymA, omcA, and narG) were responsible for VV reduction. Additionally, Polaromonas spp. was metabolically versatile and could use both organic and inorganic electron donors. The metabolic versatility of Polaromonas spp. may be important for its ability to flourish in the V tailings.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Lang Qiu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Max Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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Shen H, Wang YZ, Liu G, Li L, Xia R, Luo B, Wang J, Suo D, Shi W, Yong YC. A Whole-Cell Inorganic-Biohybrid System Integrated by Reduced Graphene Oxide for Boosting Solar Hydrogen Production. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03594] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongqiang Shen
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
- School of Material Science and Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Yan-Zhai Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Guiwu Liu
- School of Material Science and Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Longhua Li
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Rong Xia
- Zhenjiang Hengshun Bioengineering Co., Ltd, Zhenjiang 212013, P. R. China
| | - Bifu Luo
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Jixiang Wang
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku, 20520, Finland
| | - Di Suo
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Weidong Shi
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Yang-Chun Yong
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
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Metal Reduction and Protein Secretion Genes Required for Iodate Reduction by Shewanella oneidensis. Appl Environ Microbiol 2019; 85:AEM.02115-18. [PMID: 30446562 DOI: 10.1128/aem.02115-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 01/28/2023] Open
Abstract
The metal-reducing gammaproteobacterium Shewanella oneidensis reduces iodate (IO3 -) as an anaerobic terminal electron acceptor. Microbial IO3 - electron transport pathways are postulated to terminate with nitrate (NO3 -) reductase, which reduces IO3 - as an alternative electron acceptor. Recent studies with S. oneidensis, however, have demonstrated that NO3 - reductase is not involved in IO3 - reduction. The main objective of the present study was to determine the metal reduction and protein secretion genes required for IO3 - reduction by Shewanella oneidensis with lactate, formate, or H2 as the electron donor. With all electron donors, the type I and type V protein secretion mutants retained wild-type IO3 - reduction activity, while the type II protein secretion mutant lacking the outer membrane secretin GspD was impaired in IO3 - reduction. Deletion mutants lacking the cyclic AMP receptor protein (CRP), cytochrome maturation permease CcmB, and inner membrane-tethered c-type cytochrome CymA were impaired in IO3 - reduction with all electron donors, while deletion mutants lacking c-type cytochrome MtrA and outer membrane β-barrel protein MtrB of the outer membrane MtrAB module were impaired in IO3 - reduction with only lactate as an electron donor. With all electron donors, mutants lacking the c-type cytochromes OmcA and MtrC of the metal-reducing extracellular electron conduit MtrCAB retained wild-type IO3 - reduction activity. These findings indicate that IO3 - reduction by S. oneidensis involves electron donor-dependent metal reduction and protein secretion pathway components, including the outer membrane MtrAB module and type II protein secretion of an unidentified IO3 - reductase to the S. oneidensis outer membrane.IMPORTANCE Microbial iodate (IO3 -) reduction is a major component in the biogeochemical cycling of iodine and the bioremediation of iodine-contaminated environments; however, the molecular mechanism of microbial IO3 - reduction is poorly understood. Results of the present study indicate that outer membrane (type II) protein secretion and metal reduction genes encoding the outer membrane MtrAB module of the extracellular electron conduit MtrCAB are required for IO3 - reduction by S. oneidensis On the other hand, the metal-reducing c-type cytochrome MtrC of the extracellular electron conduit is not required for IO3 - reduction by S. oneidensis These findings indicate that the IO3 - electron transport pathway terminates with an as yet unidentified IO3 - reductase that associates with the outer membrane MtrAB module to deliver electrons extracellularly to IO3.
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Ferreira MR, Salgueiro CA. Biomolecular Interaction Studies Between Cytochrome PpcA From Geobacter sulfurreducens and the Electron Acceptor Ferric Nitrilotriacetate (Fe-NTA). Front Microbiol 2018; 9:2741. [PMID: 30524391 PMCID: PMC6262392 DOI: 10.3389/fmicb.2018.02741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/26/2018] [Indexed: 11/17/2022] Open
Abstract
Geobacter sulfurreducens bacterium exhibits an enormous respiratory versatility, including the utilization of several toxic and radioactive metals as electron acceptors. This versatility is also replicated in the capability of the most abundant cytochrome in G. sulfurreducens, the periplasmic triheme cytochrome PpcA, to reduce uranium, chromium and other metal ions. From all possible electron transfer pathways in G. sulfurreducens, those involved in the iron reduction are the best characterized to date. Previously, we provided structural evidence for the complex interface established between PpcA and the electron acceptor Fe(III)-citrate. However, genetic studies suggested that this acceptor is mainly reduced by outer membrane cytochomes. In the present work, we used UV-visible measurements to demonstrate that PpcA is able to directly reduce the electron acceptor ferric nitrilotriacetate (Fe-NTA), a more outer membrane permeable iron chelated form. In addition, the molecular interactions between PpcA and Fe-NTA were probed by Nuclear Magnetic Resonance (NMR) spectroscopy. The NMR spectra obtained for PpcA samples in the absence and presence of Fe-NTA showed that the interaction is reversible and encompasses a positively charged surface region located in the vicinity of the heme IV. Overall, the study elucidates the formation of an electron transfer complex between PpcA and a readily outer-membrane permeable iron chelated form. The structural and functional relationships obtained explain how a single cytochrome is designed to effectively interact with a wide range of G. sulfurreducens electron acceptors, a feature that can be explored for optimal bioelectrochemical applications.
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Affiliation(s)
- Marisa R Ferreira
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carlos A Salgueiro
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Identification of Different Putative Outer Membrane Electron Conduits Necessary for Fe(III) Citrate, Fe(III) Oxide, Mn(IV) Oxide, or Electrode Reduction by Geobacter sulfurreducens. J Bacteriol 2018; 200:JB.00347-18. [PMID: 30038047 PMCID: PMC6148476 DOI: 10.1128/jb.00347-18] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022] Open
Abstract
Gram-negative metal-reducing bacteria utilize electron conduits, chains of redox proteins spanning the outer membrane, to transfer electrons to the extracellular surface. Only one pathway for electron transfer across the outer membrane of Geobacter sulfurreducens has been linked to Fe(III) reduction. However, G. sulfurreducens is able to respire a wide array of extracellular substrates. Here we present the first combinatorial genetic analysis of five different electron conduits via creation of new markerless deletion strains and complementation vectors. Multiple conduit gene clusters appear to have overlapping roles, including two that have never been linked to metal reduction. Another recently described cluster (ExtABCD) was the only electron conduit essential during electrode reduction, a substrate of special importance to biotechnological applications of this organism. At least five gene clusters in the Geobacter sulfurreducens genome encode putative “electron conduits” implicated in electron transfer across the outer membrane, each containing a periplasmic multiheme c-type cytochrome, integral outer membrane anchor, and outer membrane redox lipoprotein(s). Markerless single-gene-cluster deletions and all possible multiple-deletion combinations were constructed and grown with soluble Fe(III) citrate, Fe(III) and Mn(IV) oxides, and graphite electrodes poised at +0.24 V and −0.1 V versus the standard hydrogen electrode (SHE). Different gene clusters were necessary for reduction of each electron acceptor. During metal oxide reduction, deletion of the previously described omcBC cluster caused defects, but deletion of additional components in an ΔomcBC background, such as extEFG, were needed to produce defects greater than 50% compared to findings with the wild type. Deletion of all five gene clusters abolished all metal reduction. During electrode reduction, only the ΔextABCD mutant had a severe growth defect at both redox potentials, while this mutation did not affect Fe(III) oxide, Mn(IV) oxide, or Fe(III) citrate reduction. Some mutants containing only one cluster were able to reduce particular terminal electron acceptors better than the wild type, suggesting routes for improvement by targeting specific electron transfer pathways. Transcriptomic comparisons between fumarate and electrode-based growth conditions showed all of these ext clusters to be constitutive, and transcriptional analysis of the triple-deletion strain containing only extABCD detected no significant changes in expression of genes encoding known redox proteins or pilus components. These genetic experiments reveal new outer membrane conduit complexes necessary for growth of G. sulfurreducens, depending on the available extracellular electron acceptor. IMPORTANCE Gram-negative metal-reducing bacteria utilize electron conduits, chains of redox proteins spanning the outer membrane, to transfer electrons to the extracellular surface. Only one pathway for electron transfer across the outer membrane of Geobacter sulfurreducens has been linked to Fe(III) reduction. However, G. sulfurreducens is able to respire a wide array of extracellular substrates. Here we present the first combinatorial genetic analysis of five different electron conduits via creation of new markerless deletion strains and complementation vectors. Multiple conduit gene clusters appear to have overlapping roles, including two that have never been linked to metal reduction. Another recently described cluster (ExtABCD) was the only electron conduit essential during electrode reduction, a substrate of special importance to biotechnological applications of this organism.
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Bylaska EJ, Rosso K. Corresponding Orbitals Derived from Periodic Bloch States for Electron Transfer Calculations of Transition Metal Oxides. J Chem Theory Comput 2018; 14:4416-4426. [PMID: 29912558 DOI: 10.1021/acs.jctc.7b01180] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An approach for modeling electron transfer in solids and at surfaces of iron-(oxyhydr)oxides and other redox active solids has been developed for electronic structure methods (i.e., plane-wave density functional theory) capable of performing calculations with periodic cells and large system sizes efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, V AB, and the electron transfer transmission factor, κel. This method is an extension of the valence bond theory electron transfer method for molecules and clusters implemented by Dupuis and others and used extensively by Rosso and co-workers in which scaled corresponding orbitals derived from the Bloch states are used to calculate the off-diagonal matrix elements H AB and S AB. A key development of the present work is the formulation of algorithms to improve the accuracy of the integration of the exact exchange integral in periodic boundary conditions. This method is demonstrated on model systems for electron small polaron transfer in iron-(oxyhydr)oxides, including bare Fe2+-Fe3+ ions, and in [Fe3+(OH2)2 (OH-)2)] nn+ chains representing the common edge-sharing Fe octahedral motif in these materials.
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17
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Rowe AR, Yoshimura M, LaRowe DE, Bird LJ, Amend JP, Hashimoto K, Nealson KH, Okamoto A. In situ
electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring. Environ Microbiol 2017; 19:2272-2285. [DOI: 10.1111/1462-2920.13723] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Annette R. Rowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Miho Yoshimura
- Department of Applied and Chemical Engineering; University of Tokyo; Tokyo Japan
| | - Doug E. LaRowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Lina J. Bird
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Jan P. Amend
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
- Department of Biological Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Kazuhito Hashimoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
| | - Kenneth H. Nealson
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Akihiro Okamoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
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Modulation of the reactivity of multiheme cytochromes by site-directed mutagenesis: moving towards the optimization of microbial electrochemical technologies. J Biol Inorg Chem 2016; 22:87-97. [DOI: 10.1007/s00775-016-1409-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023]
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Sheng A, Liu F, Xie N, Liu J. Impact of Proteins on Aggregation Kinetics and Adsorption Ability of Hematite Nanoparticles in Aqueous Dispersions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2228-2235. [PMID: 26824780 DOI: 10.1021/acs.est.5b05298] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The initial aggregation kinetics of hematite nanoparticles (NPs) that were conjugated with two model globular proteins-cytochrome c from bovine heart (Cyt) and bovine serum albumin (BSA)-were investigated over a range of monovalent (NaCl) and divalent (CaCl2) electrolyte concentrations at pH 5.7 and 9. The aggregation behavior of Cyt-NP conjugates was similar to that of bare hematite NPs, but the additional electrosteric repulsion increased the critical coagulation concentration (CCC) values from 69 mM to 113 mM in NaCl at pH 5.7. An unsaturated layer of BSA, a protein larger than Cyt, on hematite NPs resulted in fast aggregation at low salt concentrations and pH 5.7, due to the strong attractive patch-charge interaction. However, the BSA-NP conjugates could be stabilized simply by elevating salt concentrations, owing to the screening of the attractive patch-charge force and the increasing contribution from steric force. This study showed that the aggregation state of protein-conjugated NPs is proved to be completely switchable via ionic strength, pH, protein size, and protein coverage. Macroscopic Cu(II) sorption experiments further established that reducing aggregation of hematite NPs via tailoring ionic strength and protein conjugation could promote the metal uptake by hematite NPs under harsh conditions.
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Affiliation(s)
- Anxu Sheng
- School of Environmental Sciences and Engineering, Peking University , Beijing, China , 100871
| | - Feng Liu
- School of Environmental Sciences and Engineering, Peking University , Beijing, China , 100871
| | - Nan Xie
- School of Environmental Sciences and Engineering, Peking University , Beijing, China , 100871
| | - Juan Liu
- School of Environmental Sciences and Engineering, Peking University , Beijing, China , 100871
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Lai B, Yu S, Bernhardt PV, Rabaey K, Virdis B, Krömer JO. Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:39. [PMID: 26893611 PMCID: PMC4758010 DOI: 10.1186/s13068-016-0452-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/03/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Pseudomonas putida is a promising host for the bioproduction of chemicals, but its industrial applications are significantly limited by its obligate aerobic character. The aim of this paper is to empower the anoxic metabolism of wild-type Pseudomonas putida to enable bioproduction anaerobically, with the redox power from a bioelectrochemical system (BES). RESULTS The obligate aerobe Pseudomonas putida F1 was able to survive and produce almost exclusively 2-Keto-gluconate from glucose under anoxic conditions due to redox balancing with electron mediators in a BES. 2-Keto-gluconate, a precursor for industrial anti-oxidant production, was produced at an overall carbon yield of over 90 % based on glucose. Seven different mediator compounds were tested, and only those with redox potential above 0.207 V (vs standard hydrogen electrode) showed interaction with the cells. The productivity increased with the increasing redox potential of the mediator, indicating this was a key factor affecting the anoxic production process. P. putida cells survived under anaerobic conditions, and limited biofilm formation could be observed on the anode's surface. Analysis of the intracellular pools of ATP, ADP and AMP showed that cells had an increased adenylate energy charge suggesting that cells were able to generate energy using the anode as terminal electron acceptor. The analysis of NAD(H) and NADP(H) showed that in the presence of specific extracellular electron acceptors, the NADP(H) pool was more oxidised, while the NAD(H) pool was unchanged. This implies a growth limitation under anaerobic conditions due to a shortage of NADPH and provides a way to limit biomass formation, while allowing cell maintenance and catalysis at high purity and yield. CONCLUSIONS For the first time, this study proved the principle that a BES-driven bioconversion of glucose can be achieved for a wild-type obligate aerobe. This non-growth bioconversion was in high yields, high purity and also could deliver the necessary metabolic energy for cell maintenance. By combining this approach with metabolic engineering strategies, this could prove to be a powerful new way to produce bio-chemicals and fuels from renewables in both high yield and high purity.
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Affiliation(s)
- Bin Lai
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
| | - Shiqin Yu
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
| | - Paul V. Bernhardt
- />School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Korneel Rabaey
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium
| | - Bernardino Virdis
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
| | - Jens O. Krömer
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
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Liu Y, Fredrickson JK, Zachara JM, Shi L. Direct involvement of ombB, omaB, and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA. Front Microbiol 2015; 6:1075. [PMID: 26483786 PMCID: PMC4589669 DOI: 10.3389/fmicb.2015.01075] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022] Open
Abstract
The tandem gene clusters orfR-ombB-omaB-omcB and orfS-ombC-omaC-omcC of the metal-reducing bacterium Geobacter sulfurreducens PCA are responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III)-citrate and ferrihydrite [a poorly crystalline Fe(III) oxide]. Each gene cluster encodes a putative transcriptional factor (OrfR/OrfS), a porin-like outer-membrane protein (OmbB/OmbC), a periplasmic c-type cytochrome (c-Cyt, OmaB/OmaC) and an outer-membrane c-Cyt (OmcB/OmcC). The individual roles of OmbB, OmaB and OmcB in extracellular reduction of Fe(III), however, have remained either uninvestigated or controversial. Here, we showed that replacements of ombB, omaB, omcB, and ombB-omaB with an antibiotic gene in the presence of ombC-omaC-omcC had no impact on reduction of Fe(III)-citrate by G. sulfurreducens PCA. Disruption of ombB, omaB, omcB, and ombB-omaB in the absence of ombC-omaC-omcC, however, severely impaired the bacterial ability to reduce Fe(III)-citrate as well as ferrihydrite. These results unequivocally demonstrate an overlapping role of ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III) reduction by G. sulfurreducens PCA. Involvement of both ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III) reduction reflects the importance of these trans-outer membrane protein complexes in the physiology of this bacterium. Moreover, the kinetics of Fe(III)-citrate and ferrihydrite reduction by these mutants in the absence of ombC-omaC-omcC were nearly identical, which suggests that absence of any protein subunit eliminates function of OmaB/OmbB/OmcB protein complex. Finally, orfS was found to have a negative impact on the extracellular reduction of Fe(III)-citrate and ferrihydrite in G. sulfurreducens PCA probably by serving as a transcriptional repressor.
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Affiliation(s)
- Yimo Liu
- Pacific Northwest National Laboratory, Richland, WA USA
| | | | | | - Liang Shi
- Pacific Northwest National Laboratory, Richland, WA USA
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23
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Research of Iron Reduction and the Iron Reductase Localization of Anammox Bacteria. Curr Microbiol 2014; 69:880-7. [DOI: 10.1007/s00284-014-0668-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/15/2014] [Indexed: 10/24/2022]
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Membrane permeabilization underlies the enhancement of extracellular bioactivity in Shewanella oneidensis by a membrane-spanning conjugated oligoelectrolyte. Appl Microbiol Biotechnol 2014; 98:9021-31. [DOI: 10.1007/s00253-014-5973-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/01/2014] [Accepted: 07/19/2014] [Indexed: 01/29/2023]
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25
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Yang S, Bai G, Chen L, Shen Q, Diao X, Zhao G. The interaction of phenolic acids with Fe(III) in the presence of citrate as studied by isothermal titration calorimetry. Food Chem 2014; 157:302-9. [PMID: 24679785 DOI: 10.1016/j.foodchem.2014.02.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 01/31/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Under physiological conditions, exogenous chelators such as polyphenols might interact with non-protein bound ferric complexes, such as Fe(III)-citrate. Additionally, Fe(III) and citrate are widely distributed in various fruits and vegetables which are also rich in phenolic acids. In this study, we focus on the interaction between phenolic acids (gallic acid, methyl gallate and protocatechuic acid) and Fe(III) in the presence of excessive citrate by isothermal titration calorimetry (ITC) for thermodynamic studies, and stopped-flow absorption spectrometry for fast kinetic studies. Results reveal that all of these three phenolic acids can bind to the Fe(III) with the same stoichiometry (3:1). Moreover, the binding constants of these three compounds with Fe(III) are greatly dependent on ligand structure, and are much higher than that of Fe(III)-citrate. Based on their stoichiometry and superhigh binding constants, it is most likely that these three phenolic acids can displace the citrate to bind with one iron(III) ion to form a stable octahedral geometric structure, albeit at different rates. These findings shed light on the interaction between phenolic acids and Fe(III) in the presence of citrate under either physiological conditions or in a food system.
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Affiliation(s)
- Senpei Yang
- CAU & ACC Joint-Laboratory of Space Food, College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, China
| | - Guangling Bai
- CAU & ACC Joint-Laboratory of Space Food, College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, China
| | - Lingli Chen
- CAU & ACC Joint-Laboratory of Space Food, College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, China
| | - Qun Shen
- CAU & ACC Joint-Laboratory of Space Food, College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, China
| | - Xianmin Diao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, The Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Guanghua Zhao
- CAU & ACC Joint-Laboratory of Space Food, College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, China.
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Liu J, Pearce CI, Liu C, Wang Z, Shi L, Arenholz E, Rosso KM. Fe3–xTixO4 Nanoparticles as Tunable Probes of Microbial Metal Oxidation. J Am Chem Soc 2013; 135:8896-907. [DOI: 10.1021/ja4015343] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Liu
- Pacific Northwest
National Laboratory,
Richland, Washington 99352, United States
| | - Carolyn I. Pearce
- Pacific Northwest
National Laboratory,
Richland, Washington 99352, United States
| | - Chongxuan Liu
- Pacific Northwest
National Laboratory,
Richland, Washington 99352, United States
| | - Zheming Wang
- Pacific Northwest
National Laboratory,
Richland, Washington 99352, United States
| | - Liang Shi
- Pacific Northwest
National Laboratory,
Richland, Washington 99352, United States
| | - Elke Arenholz
- Advanced Light Source, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin M. Rosso
- Pacific Northwest
National Laboratory,
Richland, Washington 99352, United States
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Genomic plasticity enables a secondary electron transport pathway in Shewanella oneidensis. Appl Environ Microbiol 2012; 79:1150-9. [PMID: 23220953 DOI: 10.1128/aem.03556-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial dissimilatory iron reduction is an important biogeochemical process. It is physiologically challenging because iron occurs in soils and sediments in the form of insoluble minerals such as hematite or ferrihydrite. Shewanella oneidensis MR-1 evolved an extended respiratory chain to the cell surface to reduce iron minerals. Interestingly, the organism evolved a similar strategy for reduction of dimethyl sulfoxide (DMSO), which is reduced at the cell surface as well. It has already been established that electron transfer through the outer membrane is accomplished via a complex in which β-barrel proteins enable interprotein electron transfer between periplasmic oxidoreductases and cell surface-localized terminal reductases. MtrB is the β-barrel protein that is necessary for dissimilatory iron reduction. It forms a complex together with the periplasmic decaheme c-type cytochrome MtrA and the outer membrane decaheme c-type cytochrome MtrC. Consequently, mtrB deletion mutants are unable to reduce ferric iron. The data presented here show that this inability can be overcome by a mobile genomic element with the ability to activate the expression of downstream genes and which is inserted within the SO4362 gene of the SO4362-to-SO4357 gene cluster. This cluster carries genes similar to mtrA and mtrB and encoding a putative cell surface DMSO reductase. Expression of SO4359 and SO4360 alone was sufficient to complement not only an mtrB mutant under ferric citrate-reducing conditions but also a mutant that furthermore lacks any outer membrane cytochromes. Hence, the putative complex formed by the SO4359 and SO4360 gene products is capable not only of membrane-spanning electron transfer but also of reducing extracellular electron acceptors.
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28
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Development of a proteoliposome model to probe transmembrane electron-transfer reactions. Biochem Soc Trans 2012; 40:1257-60. [DOI: 10.1042/bst20120116] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decahaem cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system has been developed that contains Methyl Viologen as an internalized electron carrier and valinomycin as a membrane-associated cation exchanger. These proteoliposomes can be used as a model system to investigate MtrCAB function.
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Shi Z, Zachara JM, Shi L, Wang Z, Moore DA, Kennedy DW, Fredrickson JK. Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:11644-11652. [PMID: 22985396 DOI: 10.1021/es301544b] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Flavins are secreted by the dissimilatory iron-reducing bacterium Shewanella and can function as endogenous electron transfer mediators. To assess the potential importance of flavins in Fe(III) bioreduction, we investigated the redox reaction kinetics of reduced flavin mononucleotide (i.e., FMNH(2)) and reduced riboflavin (i.e., RBFH(2)) with ferrihydrite and lepidocrocite. The organic reductants rapidly reduced and dissolved ferrihydrite and lepidocrocite in the pH range 4-8. The rate constant k for 2-line ferrihydrite reductive dissolution by FMNH(2) was 87.5 ± 3.5 M(-1)·s(-1) at pH 7.0 in batch reactors, and k was similar for RBFH(2). For lepidocrocite, k was 500 ± 61 M(-1)·s(-1) for FMNH(2) and 236 ± 22 M(-1)·s(-1) for RBFH(2). The surface area normalized initial reaction rates (r(a)) were between 0.08 and 77 μmol·m(-2)·s(-1) for various conditions in stopped-flow experiments. Initial rates (r(o)) were first-order with respect to iron(III) oxide concentration, and r(a) increased with decreasing pH. Poorly crystalline 2-line ferrihydrite yielded the highest r(a), followed by more crystalline 6-line ferrihydrite and crystalline lepidocrocite. Compared to a previous whole-cell study with Shewanella oneidensis strain MR-1, our findings suggest that the reduction of electron transfer mediators by the Mtr (i.e., metal-reducing) pathway coupled to lactate oxidation is rate limiting, rather than heterogeneous electron transfer to the iron(III) oxide.
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Affiliation(s)
- Zhi Shi
- Pacific Northwest National Laboratory, P.O. Box 999, MS K8-96, Richland, Washington 99352, USA.
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Edwards MJ, Hall A, Shi L, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ, Clarke TA. The crystal structure of the extracellular 11-heme cytochrome UndA reveals a conserved 10-heme motif and defined binding site for soluble iron chelates. Structure 2012; 20:1275-84. [PMID: 22682743 DOI: 10.1016/j.str.2012.04.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/31/2012] [Accepted: 04/23/2012] [Indexed: 10/28/2022]
Abstract
Members of the genus Shewanella translocate deca- or undeca-heme cytochromes to the external cell surface thus enabling respiration using extracellular minerals and polynuclear Fe(III) chelates. The high resolution structure of the first undeca-heme outer membrane cytochrome, UndA, reveals a crossed heme chain with four potential electron ingress/egress sites arranged within four domains. Sequence and structural alignment of UndA and the deca-heme MtrF reveals the extra heme of UndA is inserted between MtrF hemes 6 and 7. The remaining UndA hemes can be superposed over the heme chain of the decaheme MtrF, suggesting that a ten heme core is conserved between outer membrane cytochromes. The UndA structure has also been crystallographically resolved in complex with substrates, an Fe(III)-nitrilotriacetate dimer or an Fe(III)-citrate trimer. The structural resolution of these UndA-Fe(III)-chelate complexes provides a rationale for previous kinetic measurements on UndA and other outer membrane cytochromes.
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Affiliation(s)
- Marcus J Edwards
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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31
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Saraiva IH, Newman DK, Louro RO. Functional characterization of the FoxE iron oxidoreductase from the photoferrotroph Rhodobacter ferrooxidans SW2. J Biol Chem 2012; 287:25541-8. [PMID: 22661703 DOI: 10.1074/jbc.m112.360636] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Photoferrotrophy is presumed to be an ancient type of photosynthetic metabolism in which bacteria use the reducing power of ferrous iron to drive carbon fixation. In this work the putative iron oxidoreductase of the photoferrotroph Rhodobacter ferrooxidans SW2 was cloned, purified, and characterized for the first time. This protein, FoxE, was characterized using spectroscopic, thermodynamic, and kinetic techniques. It is a c-type cytochrome that forms a trimer or tetramer in solution; the two hemes of each monomer are hexacoordinated by histidine and methionine. The hemes have positive reduction potentials that allow downhill electron transfer from many geochemically relevant ferrous iron forms to the photosynthetic reaction center. The reduction potentials of the hemes are different and are cross-assigned to fast and slow kinetic phases of ferrous iron oxidation in vitro. Lower reactivity was observed at high pH and may contribute to prevent ferric iron precipitation inside or at the surface of the cell. These results help fill in the molecular details of a metabolic process that likely contributed to the deposition of precambrian banded iron formations, globally important sedimentary rocks that are found on every continent today.
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Affiliation(s)
- Ivo H Saraiva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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32
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Exploring the biochemistry at the extracellular redox frontier of bacterial mineral Fe(III) respiration. Biochem Soc Trans 2012; 40:493-500. [DOI: 10.1042/bst20120018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many species of the bacterial Shewanella genus are notable for their ability to respire in anoxic environments utilizing insoluble minerals of Fe(III) and Mn(IV) as extracellular electron acceptors. In Shewanella oneidensis, the process is dependent on the decahaem electron-transport proteins that lie at the extracellular face of the outer membrane where they can contact the insoluble mineral substrates. These extracellular proteins are charged with electrons provided by an inter-membrane electron-transfer pathway that links the extracellular face of the outer membrane with the inner cytoplasmic membrane and thereby intracellular electron sources. In the present paper, we consider the common structural features of two of these outer-membrane decahaem cytochromes, MtrC and MtrF, and bring this together with biochemical, spectroscopic and voltammetric data to identify common and distinct properties of these prototypical members of different clades of the outer-membrane decahaem cytochrome superfamily.
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33
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Coursolle D, Gralnick JA. Reconstruction of Extracellular Respiratory Pathways for Iron(III) Reduction in Shewanella Oneidensis Strain MR-1. Front Microbiol 2012; 3:56. [PMID: 22363330 PMCID: PMC3282943 DOI: 10.3389/fmicb.2012.00056] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/02/2012] [Indexed: 11/13/2022] Open
Abstract
Shewanella oneidensis strain MR-1 is a facultative anaerobic bacterium capable of respiring a multitude of electron acceptors, many of which require the Mtr respiratory pathway. The core Mtr respiratory pathway includes a periplasmic c-type cytochrome (MtrA), an integral outer-membrane β-barrel protein (MtrB), and an outer-membrane-anchored c-type cytochrome (MtrC). Together, these components facilitate transfer of electrons from the c-type cytochrome CymA in the cytoplasmic membrane to electron acceptors at and beyond the outer-membrane. The genes encoding these core proteins have paralogs in the S. oneidensis genome (mtrB and mtrA each have four while mtrC has three) and some of the paralogs of mtrC and mtrA are able to form functional Mtr complexes. We demonstrate that of the additional three mtrB paralogs found in the S. oneidensis genome, only MtrE can replace MtrB to form a functional respiratory pathway to soluble iron(III) citrate. We also evaluate which mtrC/mtrA paralog pairs (a total of 12 combinations) are able to form functional complexes with endogenous levels of mtrB paralog expression. Finally, we reconstruct all possible functional Mtr complexes and test them in a S. oneidensis mutant strain where all paralogs have been eliminated from the genome. We find that each combination tested with the exception of MtrA/MtrE/OmcA is able to reduce iron(III) citrate at a level significantly above background. The results presented here have implications toward the evolution of anaerobic extracellular respiration in Shewanella and for future studies looking to increase the rates of substrate reduction for water treatment, bioremediation, or electricity production.
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Affiliation(s)
- Dan Coursolle
- Department of Microbiology, BioTechnology Institute, University of Minnesota Twin Cities St. Paul, MN, USA
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34
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Shi L, Rosso KM, Clarke TA, Richardson DJ, Zachara JM, Fredrickson JK. Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella Oneidensis MR-1. Front Microbiol 2012; 3:50. [PMID: 22363328 PMCID: PMC3279761 DOI: 10.3389/fmicb.2012.00050] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 01/30/2012] [Indexed: 11/25/2022] Open
Abstract
In the absence of O2 and other electron acceptors, the Gram-negative bacterium Shewanella oneidensis MR-1 can use ferric [Fe(III)] (oxy)(hydr)oxide minerals as the terminal electron acceptors for anaerobic respiration. At circumneutral pH and in the absence of strong complexing ligands, Fe(III) oxides are relatively insoluble and thus are external to the bacterial cells. S. oneidensis MR-1 and related strains of metal-reducing Shewanella have evolved machinery (i.e., metal-reducing or Mtr pathway) for transferring electrons from the inner-membrane, through the periplasm and across the outer-membrane to the surface of extracellular Fe(III) oxides. The protein components identified to date for the Mtr pathway include CymA, MtrA, MtrB, MtrC, and OmcA. CymA is an inner-membrane tetraheme c-type cytochrome (c-Cyt) that belongs to the NapC/NrfH family of quinol dehydrogenases. It is proposed that CymA oxidizes the quinol in the inner-membrane and transfers the released electrons to MtrA either directly or indirectly through other periplasmic proteins. A decaheme c-Cyt, MtrA is thought to be embedded in the trans outer-membrane and porin-like protein MtrB. Together, MtrAB deliver the electrons through the outer-membrane to the MtrC and OmcA on the outmost bacterial surface. MtrC and OmcA are the outer-membrane decaheme c-Cyts that are translocated across the outer-membrane by the bacterial type II secretion system. Functioning as terminal reductases, MtrC and OmcA can bind the surface of Fe(III) oxides and transfer electrons directly to these minerals via their solvent-exposed hemes. To increase their reaction rates, MtrC and OmcA can use the flavins secreted by S. oneidensis MR-1 cells as diffusible co-factors for reduction of Fe(III) oxides. Because of their extracellular location and broad redox potentials, MtrC and OmcA can also serve as the terminal reductases for soluble forms of Fe(III). In addition to Fe(III) oxides, Mtr pathway is also involved in reduction of manganese oxides and other metals. Although our understanding of the Mtr pathway is still far from complete, it is the best characterized microbial pathway used for extracellular electron exchange. Characterizations of the Mtr pathway have made significant contributions to the molecular understanding of microbial reduction of Fe(III) oxides.
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Affiliation(s)
- Liang Shi
- Pacific Northwest National Laboratory Richland, WA, USA
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35
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Liu J, Wang Z, Belchik SM, Edwards MJ, Liu C, Kennedy DW, Merkley ED, Lipton MS, Butt JN, Richardson DJ, Zachara JM, Fredrickson JK, Rosso KM, Shi L. Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1. Front Microbiol 2012; 3:37. [PMID: 22347878 PMCID: PMC3274759 DOI: 10.3389/fmicb.2012.00037] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 01/23/2012] [Indexed: 11/13/2022] Open
Abstract
The Gram-negative bacterium Sideroxydans lithotrophicus ES-1 (ES-1) grows on FeCO(3) or FeS at oxic-anoxic interfaces at circumneutral pH, and the ES-1-mediated Fe(II) oxidation occurs extracellularly. However, the molecular mechanisms underlying ES-1's ability to oxidize Fe(II) remain unknown. Survey of the ES-1 genome for candidate genes for microbial extracellular Fe(II) oxidation revealed that it contained a three-gene cluster encoding homologs of Shewanella oneidensis MR-1 (MR-1) MtrA, MtrB, and CymA that are involved in extracellular Fe(III) reduction. Homologs of MtrA and MtrB were also previously shown to be involved in extracellular Fe(II) oxidation by Rhodopseudomonas palustris TIE-1. To distinguish them from those found in MR-1, the identified homologs were named MtoAB and CymA(ES-1). Cloned mtoA partially complemented an MR-1 mutant without MtrA with regards to ferrihydrite reduction. Characterization of purified MtoA showed that it was a decaheme c-type cytochrome and oxidized soluble Fe(II). Oxidation of Fe(II) by MtoA was pH- and Fe(II)-complexing ligand-dependent. Under conditions tested, MtoA oxidized Fe(II) from pH 7 to pH 9 with the optimal rate at pH 9. MtoA oxidized Fe(II) complexed with different ligands at different rates. The reaction rates followed the order Fe(II)Cl(2) > Fe(II)-citrate > Fe(II)-NTA > Fe(II)-EDTA with the second-order rate constants ranging from 6.3 × 10(-3) μM(-1) s(-1) for oxidation of Fe(II)Cl(2) to 1.0 × 10(-3) μM(-1) s(-1) for oxidation of Fe(II)-EDTA. Thermodynamic modeling showed that redox reaction rates for the different Fe(II)-complexes correlated with their respective estimated reaction-free energies. Collectively, these results demonstrate that MtoA is a functional Fe(II)-oxidizing protein that, by working in concert with MtoB and CymA(ES-1), may oxidize Fe(II) at the bacterial surface and transfer released electrons across the bacterial cell envelope to the quinone pool in the inner membrane during extracellular Fe(II) oxidation by ES-1.
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Affiliation(s)
- Juan Liu
- Pacific Northwest National Laboratory Richland, WA, USA
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Lee JH, Kennedy DW, Dohnalkova A, Moore DA, Nachimuthu P, Reed SB, Fredrickson JK. Manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction. Environ Microbiol 2011; 13:3275-88. [PMID: 21951417 DOI: 10.1111/j.1462-2920.2011.02587.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1 produced γ-MnS (rambergite) nanoparticles during the concurrent reduction of MnO₂ and thiosulfate coupled to H₂ oxidation. To investigate effect of direct microbial reduction of MnO₂ on MnS formation, two MR-1 mutants defective in outer membrane c-type cytochromes (ΔmtrC/ΔomcA and ΔmtrC/ΔomcA/ΔmtrF) were also used and it was determined that direct reduction of MnO₂ was dominant relative to chemical reduction by biogenic sulfide generated from thiosulfate reduction. Although bicarbonate was excluded from the medium, incubations of strain MR-1 with lactate as the electron donor produced MnCO₃ (rhodochrosite) as well as MnS in nearly equivalent amounts as estimated by micro X-ray diffraction (micro-XRD) analysis. It was concluded that carbonate released from lactate metabolism promoted MnCO₃ formation and that Mn(II) mineralogy was strongly affected by carbonate ions even in the presence of abundant sulfide and weakly alkaline conditions expected to favour the precipitation of MnS. Formation of MnS, as determined by a combination of micro-XRD, transmission electron microscopy, energy dispersive X-ray spectroscopy, and selected area electron diffraction analyses was consistent with equilibrium speciation modelling predictions. Biogenic manganese sulfide may be a manganese sink in the Mn biogeochemical cycle in select environments such as deep anoxic marine basins within the Baltic Sea.
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Affiliation(s)
- Ji-Hoon Lee
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Qian Y, Shi L, Tien M. SO2907, a putative TonB-dependent receptor, is involved in dissimilatory iron reduction by Shewanella oneidensis strain MR-1. J Biol Chem 2011; 286:33973-80. [PMID: 21813652 DOI: 10.1074/jbc.m111.262113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Shewanella oneidensis strain MR-1 utilizes soluble and insoluble ferric ions as terminal electron acceptors during anaerobic respiration. The components of respiratory metabolism are localized in the membrane fractions which include the outer membrane and cytoplasmic membrane. Many of the biological components that interact with the various iron forms are proposed to be localized in these membrane fractions. To identify the iron-binding proteins acting either as an iron transporter or as a terminal iron reductase, we used metal-catalyzed oxidation reactions. This system catalyzed the oxidation of amino acids in close proximity to the iron binding site. The carbonyl groups formed from this oxidation can then be labeled with fluoresceinamine (FLNH(2)). The peptide harboring the FLNH(2) can then be proteolytically digested, purified by HPLC and then identified by MALDI-TOF tandem MS. A predominant peptide was identified to be part of SO2907 that encodes a putative TonB-dependent receptor. Compared with wild type (wt), the so2907 gene deletion (ΔSO2907) mutant has impaired ability to reduce soluble Fe(III), but retains the same ability to respire oxygen or fumarate as the wt. The ΔSO2907 mutant was also impacted in reduction of insoluble iron. Iron binding assays using isothermal titration calorimetry and fluorescence tryptophan quenching demonstrated that a truncated form of heterologous-expressed SO2907 that contains the Fe(III) binding site, is capable of binding soluble Fe(III) forms with K(d) of approximate 50 μm. To the best of our knowledge, this is the first report of the physiological role of SO2907 in Fe(III) reduction by MR-1.
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Affiliation(s)
- Yufeng Qian
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Purification and characterization of the [NiFe]-hydrogenase of Shewanella oneidensis MR-1. Appl Environ Microbiol 2011; 77:5584-90. [PMID: 21724888 DOI: 10.1128/aem.00260-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H(2)ase) that has been implicated in H(2) production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H(2)ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H(2)ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H(2)ase in trans restored the mutant's ability to produce H(2) at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H(2)ase coupled H(2) oxidation to reduction of Tc(VII)O(4)(-) and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H(2)ase-mediated reduction of Tc(VII)O(4)(-) but not methyl viologen. Under the conditions tested, all Tc(VII)O(4)(-) used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O(4)(-) was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ∼5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O(2)·nH(2)O, which was also the product of Tc(VII)O(4)(-) reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H(2)ase catalyzes Tc(VII)O(4)(-) reduction directly by coupling to H(2) oxidation.
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Cao B, Ahmed B, Kennedy DW, Wang Z, Shi L, Marshall MJ, Fredrickson JK, Isern NG, Majors PD, Beyenal H. Contribution of extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms to U(VI) immobilization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:5483-5490. [PMID: 21627155 DOI: 10.1021/es200095j] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The goal of this study was to quantify the contribution of extracellular polymeric substances (EPS) to U(VI) immobilization by Shewanella sp. HRCR-1. Through comparison of U(VI) immobilization using cells with bound EPS (bEPS) and cells with minimal EPS, we show that (i) bEPS from Shewanella sp. HRCR-1 biofilms contribute significantly to U(VI) immobilization, especially at low initial U(VI) concentrations, through both sorption and reduction; (ii) bEPS can be considered a functional extension of the cells for U(VI) immobilization and they likely play more important roles at lower initial U(VI) concentrations; and (iii) the U(VI) reduction efficiency is dependent upon the initial U(VI) concentration and decreases at lower concentrations. To quantify the relative contributions of sorption and reduction to U(VI) immobilization by EPS fractions, we isolated loosely associated EPS (laEPS) and bEPS from Shewanella sp. HRCR-1 biofilms grown in a hollow fiber membrane biofilm reactor and tested their reactivity with U(VI). We found that, when reduced, the isolated cell-free EPS fractions could reduce U(VI). Polysaccharides in the EPS likely contributed to U(VI) sorption and dominated the reactivity of laEPS, while redox active components (e.g., outer membrane c-type cytochromes), especially in bEPS, possibly facilitated U(VI) reduction.
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Affiliation(s)
- Bin Cao
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering and the Center for Environmental, Sediment and Aquatic Research, Washington State University, Pullman, Washington, United States
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40
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Qian Y, Paquete CM, Louro RO, Ross DE, Labelle E, Bond DR, Tien M. Mapping the iron binding site(s) on the small tetraheme cytochrome of Shewanella oneidensis MR-1. Biochemistry 2011; 50:6217-24. [PMID: 21682327 DOI: 10.1021/bi2005015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the model microbe Shewanella oneidensis, multi-heme proteins are utilized for respiratory metabolism where metals serve as the terminal electron acceptor. Among those is the periplasm-localized small tetraheme cytochrome (STC). STC has been extensively characterized structurally and electrochemically to which electron flow in and out of the protein has been modeled. However, until the present work, no kinetic studies have been performed to probe the route of electron flow or to determine the iron-binding site on STC. Using iron chelated by EDTA, NTA, or citrate, we have used chemical modification, site-directed mutagenesis along with isothermal titration calorimetry (ITC), and stopped-flow measurements to identify the iron binding site of STC. Chemical modifications of STC revealed that carboxyl groups on STC are involved in binding of EDTA-Fe(3+). Scanning mutagenesis was performed on Asp and Glu to probe the putative iron-binding site on STC. Two STC mutants (D21N; D80N) showed ∼70% decrease in observed electron transfer rate constant with EDTA-Fe(3+) from transient-state kinetic measurements. The impaired reactivity of STC (D80N/D21N) with EDTA-Fe(3+) was further confirmed by a significant decrease (>10-fold) in iron binding affinity.
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Affiliation(s)
- Yufeng Qian
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Identification and characterization of UndAHRCR-6, an outer membrane endecaheme c-type cytochrome of Shewanella sp. strain HRCR-6. Appl Environ Microbiol 2011; 77:5521-3. [PMID: 21652739 DOI: 10.1128/aem.00614-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UndA(HRCR-6) was identified from the metal-reducing bacterium Shewanella sp. strain HRCR-6. Both in vivo and in vitro characterization results indicate that UndA(HRCR-6) is an outer membrane endecaheme c-type cytochrome and probably has a key functional role in the extracellular reduction of iron [Fe(III)] oxides and uranium [U(VI)] by Shewanella sp. HRCR-6.
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42
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Abstract
Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along "nanowire" appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.
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43
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Biochemical characterization of purified OmcS, a c-type cytochrome required for insoluble Fe(III) reduction in Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:404-12. [DOI: 10.1016/j.bbabio.2011.01.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 12/14/2010] [Accepted: 01/05/2011] [Indexed: 12/18/2022]
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Zhao J, Scheibe TD, Mahadevan R. Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation. Biotechnol Bioeng 2011; 108:1537-48. [DOI: 10.1002/bit.23096] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 01/20/2011] [Accepted: 01/24/2011] [Indexed: 11/09/2022]
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45
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Firer-Sherwood MA, Bewley KD, Mock JY, Elliott SJ. Tools for resolving complexity in the electron transfer networks of multiheme cytochromes c. Metallomics 2011; 3:344-8. [PMID: 21327265 DOI: 10.1039/c0mt00097c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Examining electron transfer between two proteins with identical spectroscopic signatures is a challenging task. It is supposed that several multiheme cytochromes in Shewanella oneidensis form a molecular "wire" through which electrons are transported across the cellular space and a direct study of this transient protein-protein interaction has not yet been reported. In this study, we present variations on catalytic protein film voltammetry and an anaerobic affinity chromatography assay to demonstrate unidirectional electron transfer between proposed protein pairs. Through use of these techniques, we are able to confirm the transient interactions between these cytochromes, supporting the model of electron transfer that is present in the literature.
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46
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An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PLoS One 2010; 5:e13968. [PMID: 21103051 PMCID: PMC2980473 DOI: 10.1371/journal.pone.0013968] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 08/24/2010] [Indexed: 01/08/2023] Open
Abstract
Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300-500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella.
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47
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Abstract
Engineering efficient, directional electronic communication between living and nonliving systems has the potential to combine the unique characteristics of both materials for advanced biotechnological applications. However, the cell membrane is designed by nature to be an insulator, restricting the flow of charged species; therefore, introducing a biocompatible pathway for transferring electrons across the membrane without disrupting the cell is a significant challenge. Here we describe a genetic strategy to move intracellular electrons to an inorganic extracellular acceptor along a molecularly defined route. To do so, we reconstitute a portion of the extracellular electron transfer chain of Shewanella oneidensis MR-1 into the model microbe Escherichia coli. This engineered E. coli can reduce metal ions and solid metal oxides ∼8× and ∼4× faster than its parental strain. We also find that metal oxide reduction is more efficient when the extracellular electron acceptor has nanoscale dimensions. This work demonstrates that a genetic cassette can create a conduit for electronic communication from living cells to inorganic materials, and it highlights the importance of matching the size scale of the protein donors to inorganic acceptors.
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48
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Coursolle D, Gralnick JA. Modularity of the Mtr respiratory pathway of Shewanella oneidensis strain MR-1. Mol Microbiol 2010; 77:995-1008. [PMID: 20598084 DOI: 10.1111/j.1365-2958.2010.07266.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Four distinct pathways predicted to facilitate electron flow for respiration of externally located substrates are encoded in the genome of Shewanella oneidensis strain MR-1. Although the pathways share a suite of similar proteins, the activity of only two of these pathways has been described. Respiration of extracellular substrates requires a mechanism to facilitate electron transfer from the quinone pool in the cytoplasmic membrane to terminal reductase enzymes located on the outer leaflet of the outer membrane. The four pathways share MtrA paralogues, a periplasmic electron carrier cytochrome, and terminal reductases similar to MtrC for reduction of metals, flavins and electrodes or to DmsAB for reduction of dimethyl sulphoxide (DMSO). The promiscuity of respiratory electron transfer reactions catalysed by these pathways has made studying strains lacking single proteins difficult. Here, we present a comprehensive analysis of MtrA and MtrC paralogues in S. oneidensis to define the roles of these proteins in respiration of insoluble iron oxide, soluble iron citrate, flavins and DMSO. We present evidence that some periplasmic electron carrier components and terminal reductases in these pathways can provide partial compensation in the absence of the primary component, a phenomenon described as modularity, and discuss biochemical and evolutionary implications.
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Affiliation(s)
- Dan Coursolle
- BioTechnology Institute and Department of Microbiology, University of Minnesota-Twin Cities, St. Paul, MN 55108, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Microbiology, University of Minnesota-Twin Cities, St. Paul, MN 55108, USA
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Marshall MJ, Beliaev AS, Fredrickson JK. Microbial Transformations of Radionuclides in the Subsurface. Environ Microbiol 2010. [DOI: 10.1002/9780470495117.ch4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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Johs A, Shi L, Droubay T, Ankner J, Liang L. Characterization of the decaheme c-type cytochrome OmcA in solution and on hematite surfaces by small angle x-ray scattering and neutron reflectometry. Biophys J 2010; 98:3035-43. [PMID: 20550916 PMCID: PMC2884263 DOI: 10.1016/j.bpj.2010.03.049] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/09/2010] [Accepted: 03/16/2010] [Indexed: 11/25/2022] Open
Abstract
The outer membrane protein OmcA is an 85 kDa decaheme c-type cytochrome located on the surface of the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. It is assumed to mediate shuttling of electrons to extracellular acceptors that include solid metal oxides such as hematite (alpha-Fe(2)O(3)). No information is yet available concerning OmcA structure in physiologically relevant conditions such as aqueous environments. We purified OmcA and characterized its solution structure by small angle x-ray scattering (SAXS), and its interaction at the hematite-water interface by neutron reflectometry. SAXS showed that OmcA is a monomer that adopts a flat ellipsoidal shape with an overall dimension of 34 x 90 x 65 A(3). To our knowledge, we obtained the first direct evidence that OmcA undergoes a redox state-dependent conformational change in solution whereby reduction decreases the overall length of OmcA by approximately 7 A (the maximum dimension was 96 A for oxidized OmcA, and 89 A for NADH and dithionite-reduced OmcA). OmcA was also found to physically interact with electron shuttle molecules such as flavin mononucleotide, resulting in the formation of high-molecular-weight assemblies. Neutron reflectometry showed that OmcA forms a well-defined monomolecular layer on hematite surfaces, where it assumes an orientation that maximizes its contact area with the mineral surface. These novel insights into the molecular structure of OmcA in solution, and its interaction with insoluble hematite and small organic ligands, demonstrate the fundamental structural bases underlying OmcA's role in mediating redox processes.
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Affiliation(s)
- A. Johs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - L. Shi
- Pacific Northwest National Laboratory, Richland, Washington
| | - T. Droubay
- Pacific Northwest National Laboratory, Richland, Washington
| | - J.F. Ankner
- Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - L. Liang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
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