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Rodríguez-Torres LM, Huerta-Miranda GA, Martínez-García AL, Mazón-Montijo DA, Hernández-Eligio A, Miranda-Hernández M, Juárez K. Influence of support materials on the electroactive behavior, structure and gene expression of wild type and GSU1771-deficient mutant of Geobacter sulfurreducens biofilms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33612-3. [PMID: 38758442 DOI: 10.1007/s11356-024-33612-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/05/2024] [Indexed: 05/18/2024]
Abstract
Geobacter sulfurreducens DL1 is a metal-reducing dissimilatory bacterium frequently used to produce electricity in bioelectrochemical systems (BES). The biofilm formed on electrodes is one of the most important factors for efficient electron transfer; this is possible due to the production of type IV pili and c-type cytochromes that allow it to carry out extracellular electron transfer (EET) to final acceptors. In this study, we analyzed the biofilm formed on different support materials (glass, hematite (Fe2O3) on glass, fluorine-doped tin oxide (FTO) semiconductor glass, Fe2O3 on FTO, graphite, and stainless steel) by G. sulfurreducens DL1 (WT) and GSU1771-deficient strain mutant (Δgsu1771). GSU1771 is a transcriptional regulator that controls the expression of several genes involved in electron transfer. Different approaches and experimental tests were carried out with the biofilms grown on the different support materials including structure analysis by confocal laser scanning microscopy (CLSM), characterization of electrochemical activity, and quantification of relative gene expression by RT-qPCR. The gene expression of selected genes involved in EET was analyzed, observing an overexpression of pgcA, omcS, omcM, and omcF from Δgsu1771 biofilms compared to those from WT, also the overexpression of the epsH gene, which is involved in exopolysaccharide synthesis. Although we observed that for the Δgsu1771 mutant strain, the associated redox processes are similar to the WT strain, and more current is produced, we think that this could be associated with a higher relative expression of certain genes involved in EET and in the production of exopolysaccharides despite the chemical environment where the biofilm develops. This study supports that G. sulfurreducens is capable of adapting to the electrochemical environment where it grows.
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Affiliation(s)
- Luis Miguel Rodríguez-Torres
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Guillermo Antonio Huerta-Miranda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Ana Luisa Martínez-García
- Centro de Investigación en Materiales Avanzados S. C., Subsede Monterrey, Grupo de Investigación DORA-Lab, 66628, Apodaca, N. L, México
- Centro de Investigación e Innovación Tecnológica (CIIT), Grupo de Investigación DORA-Lab, Tecnológico Nacional de México Campus Nuevo León (TECNL), 66629, Apodaca, N. L, México
| | - Dalia Alejandra Mazón-Montijo
- Centro de Investigación en Materiales Avanzados S. C., Subsede Monterrey, Grupo de Investigación DORA-Lab, 66628, Apodaca, N. L, México
- Centro de Investigación e Innovación Tecnológica (CIIT), Grupo de Investigación DORA-Lab, Tecnológico Nacional de México Campus Nuevo León (TECNL), 66629, Apodaca, N. L, México
- Investigadores Por México, CONAHCYT, Ciudad de México, México
| | - Alberto Hernández-Eligio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, México
- Investigadores Por México, CONAHCYT, Ciudad de México, México
| | - Margarita Miranda-Hernández
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Priv. Xochicalco, 62580, Temixco, Morelos, México
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, México.
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Jaramillo-Rodríguez JB, Vega-Alvarado L, Rodríguez-Torres LM, Huerta-Miranda GA, Hernández-Eligio A, Juarez K. Global transcriptional analysis of Geobacter sulfurreducens gsu1771 mutant biofilm grown on two different support structures. PLoS One 2023; 18:e0293359. [PMID: 37878651 PMCID: PMC10599522 DOI: 10.1371/journal.pone.0293359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023] Open
Abstract
Electroactive biofilms formation by the metal-reducing bacterium Geobacter sulfurreducens is a step crucial for bioelectricity generation and bioremediation. The transcriptional regulator GSU1771 controls the expression of essential genes involved in electron transfer and biofilm formation in G. sulfurreducens, with GSU1771-deficient producing thicker and more electroactive biofilms. Here, RNA-seq analyses were conducted to compare the global gene expression patterns of wild-type and Δgsu1771 mutant biofilms grown on non-conductive (glass) and conductive (graphite electrode) materials. The Δgsu1771 biofilm grown on the glass surface exhibited 467 differentially expressed (DE) genes (167 upregulated and 300 downregulated) versus the wild-type biofilm. In contrast, the Δgsu1771 biofilm grown on the graphite electrode exhibited 119 DE genes (79 upregulated and 40 downregulated) versus the wild-type biofilm. Among these DE genes, 67 were also differentially expressed in the Δgsu1771 biofilm grown on glass (56 with the same regulation and 11 exhibiting counter-regulation). Among the upregulated genes in the Δgsu1771 biofilms, we identified potential target genes involved in exopolysaccharide synthesis (gsu1961-63, gsu1959, gsu1972-73, gsu1976-77). RT-qPCR analyses were then conducted to confirm the differential expression of a selection of genes of interest. DNA-protein binding assays demonstrated the direct binding of the GSU1771 regulator to the promoter region of pgcA, pulF, relA, and gsu3356. Furthermore, heme-staining and western blotting revealed an increase in c-type cytochromes including OmcS and OmcZ in Δgsu1771 biofilms. Collectively, our findings demonstrated that GSU1771 is a global regulator that controls extracellular electron transfer and exopolysaccharide synthesis in G. sulfurreducens, which is crucial for electroconductive biofilm development.
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Affiliation(s)
- Juan B. Jaramillo-Rodríguez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Luis M. Rodríguez-Torres
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Guillermo A. Huerta-Miranda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alberto Hernández-Eligio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Investigador por México, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Katy Juarez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Howley E, Krajmalnik-Brown R, Torres CI. Cytochrome gene expression shifts in Geobacter sulfurreducens to maximize energy conservation in response to changes in redox conditions. Biosens Bioelectron 2023; 237:115524. [PMID: 37459687 DOI: 10.1016/j.bios.2023.115524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/19/2023] [Accepted: 07/07/2023] [Indexed: 08/13/2023]
Abstract
Previous studies have identified that Geobacter sulfurreducens has three different electron transfer pathways for respiration, and it switches between these pathways to adapt to the redox potential of its electron acceptor. However, only a small fraction of the electron carriers from each pathway have been identified. In this study, we combined electrochemical and gene expression data to identify electron carriers in the inner membrane, periplasm, outer membrane, and exterior of the cell that may be induced by the use of the three different electron transfer pathways. Cyclic voltammetry was performed on thin biofilms grown on anodes poised at different redox potentials, providing a quantitative assessment of the relative use of three electron-transfer pathways in each condition (catalytic midpoint potentials (EKAs) of -0.227 V [Low], -0.15 V [Medium], -0.1 V [High] vs. SHE). Transcriptomic analyses as a function of electrochemical signals or fumarate utilization showed differential induction in inner membrane (Medium: cbcL), periplasmic (Low: ppcB/ppcE, Medium: ppcA), outer membrane (Low: extA/extC, Medium: extJ/extK, Fumarate: extF/extG), and extracellular (Medium: omcZ, High/Fumarate: omcS/omcT) cytochromes, suggesting the pathway signals are associated with complex transcriptomic responses in genes across the electron transfer pathway. Our method combining electrochemical modeling and transcriptomics could be adapted to better understand electron transport in other electroactive organisms with complex metabolisms.
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Affiliation(s)
- Ethan Howley
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Rosa Krajmalnik-Brown
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA; Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - César I Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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Abstract
Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.
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Affiliation(s)
- J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA; ,
| | - D R Bond
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA; ,
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Wang F, Craig L, Liu X, Rensing C, Egelman EH. Microbial nanowires: type IV pili or cytochrome filaments? Trends Microbiol 2023; 31:384-392. [PMID: 36446702 PMCID: PMC10033339 DOI: 10.1016/j.tim.2022.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
A dynamic field of study has emerged involving long-range electron transport by extracellular filaments in anaerobic bacteria, with Geobacter sulfurreducens being used as a model system. The interest in this topic stems from the potential uses of such systems in bioremediation, energy generation, and new bio-based nanotechnology for electronic devices. These conductive extracellular filaments were originally thought, based upon low-resolution observations of dried samples, to be type IV pili (T4P). However, the recently published atomic structure for the T4P from G. sulfurreducens, obtained by cryo-electron microscopy (cryo-EM), is incompatible with the numerous models that have been put forward for electron conduction. As with all high-resolution structures of T4P, the G. sulfurreducens T4P structure shows a partial melting of the α-helix that substantially impacts the aromatic residue positions such that they are incompatible with conductivity. Furthermore, new work using high-resolution cryo-EM shows that conductive filaments thought to be T4P are actually polymerized cytochromes, with stacked heme groups forming a continuous conductive wire, or extracellular DNA. Recent atomic structures of three different cytochrome filaments from G. sulfurreducens suggest that such polymers evolved independently on multiple occasions. The expectation is that such polymerized cytochromes may be found emanating from other anaerobic organisms.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
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Gu Y, Qi X, Yang X, Jiang Y, Liu P, Quan X, Liang P. Extracellular electron transfer and the conductivity in microbial aggregates during biochemical wastewater treatment: A bottom-up analysis of existing knowledge. WATER RESEARCH 2023; 231:119630. [PMID: 36689883 DOI: 10.1016/j.watres.2023.119630] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/14/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Microbial extracellular electron transfer (EET) plays a crucial role in bioenergy production and resource recovery from wastewater. Interdisciplinary efforts have been made to unveil EET processes at various spatial scales, from nanowires to microbial aggregates. Electrical conductivity has been frequently measured as an indicator of EET efficiency. In this review, the conductivity of nanowires, biofilms, and granular sludge was summarized, and factors including subjects, measurement methods, and conducting conditions that affect the conductivity difference were discussed in detail. The high conductivity of nanowires does not necessarily result in efficient EET in microbial aggregates due to the existence of non-conductive substances and contact resistance. Improving the conductivity measurement of microbial aggregates is important because it enables the calculation of an EET flux from conductivity and a comparison of the flux with mass transfer coefficients. This review provides new insight into the significance, characterization, and optimization of EET in microbial aggregates during a wastewater treatment process.
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Affiliation(s)
- Yuyi Gu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xiang Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xufei Yang
- Department of Agricultural and Biosystems Engineering, South Dakota State University, Brookings, SD 57007 USA
| | - Yong Jiang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Panpan Liu
- School of Ecology and Environment, Zhengzhou University, Zhengzhou 450001, PR China
| | - Xiangchun Quan
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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Howley E, Ki D, Krajmalnik-Brown R, Torres CI. Geobacter sulfurreducens' Unique Metabolism Results in Cells with a High Iron and Lipid Content. Microbiol Spectr 2022; 10:e0259322. [PMID: 36301091 PMCID: PMC9769739 DOI: 10.1128/spectrum.02593-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/24/2022] [Indexed: 01/07/2023] Open
Abstract
Geobacter sulfurreducens is a ubiquitous iron-reducing bacterium in soils, and in engineered systems, it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work, we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C, H, O, N, and ash content) showed high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 ± 0.2 μg/g dry weight) and lipids (32 ± 0.5% dry weight/dry weight) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. IMPORTANCE Geobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively "breathing" metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal and, as a ubiquitous iron reducer in soils around the world, G. sulfurreducens has an impact on the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organism's composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria-these observations are important for future microbiologists and biotechnologists working with the organism.
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Affiliation(s)
- Ethan Howley
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Dongwon Ki
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Division of Living and the Built Environment Research, Seoul Institute of Technology, Seoul, South Korea
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - César I. Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Engineering of Matter Transport and Energy, Arizona State University, Tempe, Arizona, USA
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GSU1771 regulates extracellular electron transfer and electroactive biofilm formation in Geobacter sulfurreducens: Genetic and electrochemical characterization. Bioelectrochemistry 2022; 145:108101. [PMID: 35334296 DOI: 10.1016/j.bioelechem.2022.108101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/21/2022]
Abstract
Type IV pili and the >100c-type cytochromes in Geobacter sulfurreducens are essential for extracellular electron transfer (EET) towards metal oxides and electrodes. A previous report about a mutation in the gsu1771 gene indicated an enhanced reduction of insoluble Fe(III) oxides coupled with increased pilA expression. Herein, a marker-free gsu1771-deficient mutant was constructed and characterized to assess the role of this regulator in EET and the formation of electroactive biofilms. Deleting this gene delayed microbial growth in the acetate/fumarate media (electron donor and acceptor, respectively). However, this mutant reduced soluble and insoluble Fe(III) oxides more efficiently. Heme staining, western blot, and RT-qPCR analyses demonstrated that GSU1771 regulates the transcription of several genes (including pilA) and many c-type cytochromes involved in EET, suggesting the broad regulatory role of this protein. DNA-protein binding assays indicated that GSU1771 directly regulates the transcription of pilA, omcE, omcS, and omcZ. Additionally, gsu1771-deficient mutant biofilms are thicker than wild-type strains. Electrochemical studies revealed that the current produced by this biofilm was markedly higher than the wild-type strains (approximately 100-fold). Thus, demonstrating the role of GSU1771 in the EET pathway and establishing a methodology to develop highly electroactive G. sulfurreducens mutants.
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Morgado L, Salgueiro CA. Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes. Metallomics 2022; 14:6539350. [DOI: 10.1093/mtomcs/mfac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Cytochromes are electron transfer proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electron outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and elucidate the stepwise electron transfer along the respiratory paths. However, investigating direct electron transfer events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. NMR spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor electron transfer within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of electron transfer between c-type cytochromes, using as model a triheme periplasmic cytochrome (PpcA) and a membrane associated monoheme cytochrome (OmcF) from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional electron transfer within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory electron transfer chains.
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Affiliation(s)
- Leonor Morgado
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
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Hoang AT, Nižetić S, Ng KH, Papadopoulos AM, Le AT, Kumar S, Hadiyanto H, Pham VV. Microbial fuel cells for bioelectricity production from waste as sustainable prospect of future energy sector. CHEMOSPHERE 2022; 287:132285. [PMID: 34563769 DOI: 10.1016/j.chemosphere.2021.132285] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Microbial fuel cell (MFC) is lauded for its potentials to solve both energy crisis and environmental pollution. Technologically, it offers the capability to harness electricity from the chemical energy stored in the organic substrate with no intermediate steps, thereby minimizes the entropic loss due to the inter-conversion of energy. The sciences underneath such MFCs include the electron and proton generation from the metabolic decomposition of the substrate by microbes at the anode, followed by the shuttling of these charges to cathode for electricity generation. While its promising prospects were mutually evinced in the past investigations, the upscaling of MFC in sustaining global energy demands and waste treatments is yet to be put into practice. In this context, the current review summarizes the important knowledge and applications of MFCs, concurrently identifies the technological bottlenecks that restricted its vast implementation. In addition, economic analysis was also performed to provide multiangle perspectives to readers. Succinctly, MFCs are mainly hindered by the slow metabolic kinetics, sluggish transfer of charged particles, and low economic competitiveness when compared to conventional technologies. From these hindering factors, insightful strategies for improved practicality of MFCs were formulated, with potential future research direction being identified too. With proper planning, we are delighted to see the industrialization of MFCs in the near future, which would benefit the entire human race with cleaner energy and the environment.
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Affiliation(s)
- Anh Tuan Hoang
- Institute of Engineering, Ho Chi Minh City University of Technology (HUTECH), Ho Chi Minh City, Viet Nam.
| | - Sandro Nižetić
- University of Split, FESB, Rudjera Boskovica 32, 21000, Split, Croatia
| | - Kim Hoong Ng
- Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City, 24301, Taiwan.
| | - Agis M Papadopoulos
- Process Equipment Design Laboratory, Department of Mechanical Engineering, Aristotle University of Thessaloniki, Postal Address: GR-54124, Thessaloniki, Greece
| | - Anh Tuan Le
- School of Transportation Engineering, Hanoi University of Science and Technology, Hanoi, Viet Nam.
| | - Sunil Kumar
- Waste Reprocessing Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440 020, India
| | - H Hadiyanto
- Center of Biomass and Renewable Energy (CBIORE), Department of Chemical Engineering, Diponegoro University, Jl. Prof. Soedarto SH, Tembalang, Semarang, 50271, Indonesia; School of Postgraduate Studies, Diponegoro University, Jl. Imam Bardjo, SH Semarang, 50241, Indonesia.
| | - Van Viet Pham
- PATET Research Group, Ho Chi Minh City University of Transport, Ho Chi Minh City, Viet Nam.
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11
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Hu Y, Wang Y, Han X, Shan Y, Li F, Shi L. Biofilm Biology and Engineering of Geobacter and Shewanella spp. for Energy Applications. Front Bioeng Biotechnol 2021; 9:786416. [PMID: 34926431 PMCID: PMC8683041 DOI: 10.3389/fbioe.2021.786416] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/18/2021] [Indexed: 01/04/2023] Open
Abstract
Geobacter and Shewanella spp. were discovered in late 1980s as dissimilatory metal-reducing microorganisms that can transfer electrons from cytoplasmic respiratory oxidation reactions to external metal-containing minerals. In addition to mineral-based electron acceptors, Geobacter and Shewanella spp. also can transfer electrons to electrodes. The microorganisms that have abilities to transfer electrons to electrodes are known as exoelectrogens. Because of their remarkable abilities of electron transfer, Geobacter and Shewanella spp. have been the two most well studied groups of exoelectrogens. They are widely used in bioelectrochemical systems (BESs) for various biotechnological applications, such as bioelectricity generation via microbial fuel cells. These applications mostly associate with Geobacter and Shewanella biofilms grown on the surfaces of electrodes. Geobacter and Shewanella biofilms are electrically conductive, which is conferred by matrix-associated electroactive components such as c-type cytochromes and electrically conductive nanowires. The thickness and electroactivity of Geobacter and Shewanella biofilms have a significant impact on electron transfer efficiency in BESs. In this review, we first briefly discuss the roles of planktonic and biofilm-forming Geobacter and Shewanella cells in BESs, and then review biofilm biology with the focus on biofilm development, biofilm matrix, heterogeneity in biofilm and signaling regulatory systems mediating formation of Geobacter and Shewanella biofilms. Finally, we discuss strategies of Geobacter and Shewanella biofilm engineering for improving electron transfer efficiency to obtain enhanced BES performance.
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Affiliation(s)
- Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yinghui Wang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xi Han
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yawei Shan
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Feng Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China.,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan, China
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12
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Fernandes TM, Morgado L, Turner DL, Salgueiro CA. Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria. Antioxidants (Basel) 2021; 10:844. [PMID: 34070486 PMCID: PMC8227773 DOI: 10.3390/antiox10060844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023] Open
Abstract
Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.
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Affiliation(s)
- Tomás M. Fernandes
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - Leonor Morgado
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - David L. Turner
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal;
| | - Carlos A. Salgueiro
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
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13
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Abstract
Extracellular electron transfer (EET) is an important biological process in microbial physiology as found in dissimilatory metal oxidation/reduction and interspecies electron transfer in syntrophy in natural environments. EET also plays a critical role in microorganisms relevant to environmental biotechnology in metal-contaminated areas, metal corrosion, bioelectrochemical systems, and anaerobic digesters. Geobacter species exist in a diversity of natural and artificial environments. One of the outstanding features of Geobacter species is the capability of direct EET with solid electron donors and acceptors, including metals, electrodes, and other cells. Therefore, Geobacter species are pivotal in environmental biogeochemical cycles and biotechnology applications. Geobacter sulfurreducens, a representative Geobacter species, has been studied for direct EET as a model microorganism. G. sulfurreducens employs electrically conductive pili (e-pili) and c-type cytochromes for the direct EET. The biological function and electronics applications of the e-pili have been reviewed recently, and this review focuses on the cytochromes. Geobacter species have an unusually large number of cytochromes encoded in their genomes. Unlike most other microorganisms, Geobacter species localize multiple cytochromes in each subcellular fraction, outer membrane, periplasm, and inner membrane, as well as in the extracellular space, and differentially utilize these cytochromes for EET with various electron donors and acceptors. Some of the cytochromes are functionally redundant. Thus, the EET in Geobacter is complicated. Geobacter coordinates the cytochromes with other cellular components in the elaborate EET system to flourish in the environment.
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Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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14
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Sheik CS, Badalamenti JP, Telling J, Hsu D, Alexander SC, Bond DR, Gralnick JA, Lollar BS, Toner BM. Novel Microbial Groups Drive Productivity in an Archean Iron Formation. Front Microbiol 2021; 12:627595. [PMID: 33859627 PMCID: PMC8042283 DOI: 10.3389/fmicb.2021.627595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deep subsurface environments are decoupled from Earth's surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C1-C4. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H2/CO2 or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.
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Affiliation(s)
- Cody S. Sheik
- Department of Biology and the Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jon Telling
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Hsu
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Scott C. Alexander
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Daniel R. Bond
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jeffrey A. Gralnick
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | | | - Brandy M. Toner
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN, United States
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15
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Andrade A, Hernández-Eligio A, Tirado AL, Vega-Alvarado L, Olvera M, Morett E, Juárez K. Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes in Geobacter sulfurreducens. Front Microbiol 2021; 12:626443. [PMID: 33737919 PMCID: PMC7962754 DOI: 10.3389/fmicb.2021.626443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Integration host factor (IHF) is a widely distributed small heterodimeric protein member of the bacterial Nucleoid-Associated Proteins (NAPs), implicated in multiple DNA regulatory processes. IHF recognizes a specific DNA sequence and induces a large bend of the nucleic acid. IHF function has been mainly linked with the regulation of RpoN-dependent promoters, where IHF commonly recognizes a DNA sequence between the enhancer-binding region and the promoter, facilitating a close contact between the upstream bound activator and the promoter bound, RNA polymerase. In most proteobacteria, the genes encoding IHF subunits (ihfA and ihfB) are found in a single copy. However, in some Deltaproteobacteria, like Geobacter sulfurreducens, those genes are duplicated. To date, the functionality of IHF reiterated encoding genes is unknown. In this work, we achieved the functional characterization of the ihfA-1, ihfA-2, ihfB-1, and ihfB-2 from G. sulfurreducens. Unlike the ΔihfA-2 or ΔihfB-1 strains, single gene deletion in ihfA-1 or ihfB-2, provokes an impairment in fumarate and Fe(III) citrate reduction. Accordingly, sqRT-PCR experiments showed that ihfA-1 and ihfB-2 were expressed at higher levels than ihfA-2 and ihfB-1. In addition, RNA-Seq analysis of the ΔihfA-1 and ΔihfB-2 strains revealed a total of 89 and 122 differentially expressed genes, respectively. Furthermore, transcriptional changes in 25 genes were shared in both mutant strains. Among these genes, we confirmed the upregulation of the pilA-repressor, GSU1771, and downregulation of the triheme-cytochrome (pgcA) and the aconitate hydratase (acnA) genes by RT-qPCR. EMSA experiments also demonstrated the direct binding of IHF to the upstream promoter regions of GSU1771, pgcA and acnA. PilA changes in ΔihfA-1 and ΔihfB-2 strains were also verified by immunoblotting. Additionally, heme-staining of subcellular fractions in ΔihfA-1 and ΔihfB-2 strains revealed a remarkable deficit of c-type cytochromes. Overall, our data indicate that at least during fumarate and Fe(III) citrate reduction, the functional IHF regulator is likely assembled by the products of ihfA-1 and ihfB-2. Also, a role of IHF controlling expression of multiple genes (other than RpoN-dependent) affects G. sulfurreducens physiology and extracellular electron transfer.
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Affiliation(s)
- Angel Andrade
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Alberto Hernández-Eligio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,CONACYT, Ciudad de México, Mexico
| | - Ana Lilia Tirado
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Maricela Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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16
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Mollaei M, Timmers PHA, Suarez-Diez M, Boeren S, van Gelder AH, Stams AJM, Plugge CM. Comparative proteomics of Geobacter sulfurreducens PCA T in response to acetate, formate and/or hydrogen as electron donor. Environ Microbiol 2020; 23:299-315. [PMID: 33185968 PMCID: PMC7894505 DOI: 10.1111/1462-2920.15311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO2 fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO2 , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.
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Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Antonie H van Gelder
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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17
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Global transcriptional analysis of Geobacter sulfurreducens under palladium reducing conditions reveals new key cytochromes involved. Appl Microbiol Biotechnol 2020; 104:4059-4069. [DOI: 10.1007/s00253-020-10502-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 01/15/2023]
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18
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Teixeira LR, Cordas CM, Fonseca MP, Duke NEC, Pokkuluri PR, Salgueiro CA. Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens. Front Microbiol 2020; 10:2941. [PMID: 32010071 PMCID: PMC6971198 DOI: 10.3389/fmicb.2019.02941] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/06/2019] [Indexed: 11/13/2022] Open
Abstract
The monoheme outer membrane cytochrome F (OmcF) from Geobacter sulfurreducens plays an important role in Fe(III) reduction and electric current production. The electrochemical characterization of this cytochrome has shown that its redox potential is modulated by the solution pH (redox-Bohr effect) endowing the protein with the necessary properties to couple electron and proton transfer in the physiological range. The analysis of the OmcF structures in the reduced and oxidized states showed that with the exception of the side chain of histidine 47 (His47), all other residues with protonatable side chains are distant from the heme iron and, therefore, are unlikely to affect the redox potential of the protein. The protonatable site at the imidazole ring of His47 is in the close proximity to the heme and, therefore, this residue was suggested as the redox-Bohr center. In the present work, we tested this hypothesis by replacing the His47 with non-protonatable residues (isoleucine – OmcFH47I and phenylalanine – OmcFH47F). The structure of the mutant OmcFH47I was determined by X-ray crystallography to 1.13 Å resolution and showed only minimal changes at the site of the mutation. Both mutants were 15N-labeled and their overall folding was confirmed to be the same as the wild-type by NMR spectroscopy. The pH dependence of the redox potential of the mutants was measured by cyclic voltammetry. Compared to the wild-type protein, the magnitude of the redox-Bohr effect in the mutants was smaller, but not fully abolished, confirming the role of His47 on the pH modulation of OmcF’s redox potential. However, the pH effect on the heme substituents’ NMR chemical shifts suggested that the heme propionate P13 also contributes to the overall redox-Bohr effect in OmcF. In physiological terms, the contribution of two independent acid–base centers to the observed redox-Bohr effect confers OmcF a higher versatility to environmental changes by coupling electron/proton transfer within a wider pH range.
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Affiliation(s)
- Liliana R Teixeira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta P Fonseca
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Norma E C Duke
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Phani Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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19
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Huang L, Liu X, Ye Y, Chen M, Zhou S. Evidence for the coexistence of direct and riboflavin-mediated interspecies electron transfer in Geobacter co-culture. Environ Microbiol 2019; 22:243-254. [PMID: 31657092 DOI: 10.1111/1462-2920.14842] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/20/2019] [Accepted: 10/23/2019] [Indexed: 11/30/2022]
Abstract
Geobacter species can secrete free redox-active flavins, but the role of these flavins in the interspecies electron transfer (IET) of Geobacter direct interspecies electron transfer (DIET) co-culture is unknown. Here, we report the presence of a new riboflavin-mediated interspecies electron transfer (RMIET) process in a traditional Geobacter DIET co-culture; in this process, riboflavin contributes to IET by acting as a free-form electron shuttle between free Geobacter species and serving as a bound cofactor of some cytochromes in Geobacter co-culture aggregates. Multiple lines of evidence indicate that RMIET facilitates the primary initiation of syntrophic growth between Geobacter species before establishing the DIET co-culture and provides additional ways alongside the DIET to transfer electrons to achieve electric syntrophy between Geobacter species. Redox kinetic analysis of riboflavin on either Geobacter species demonstrated that the Gmet_2896 cytochrome acts as the key riboflavin reduction site, while riboflavin oxidation by Geobacter sulfurreducens is the rate-limiting step in RMIET, and the RMIET makes only a minor contribution to IET in Geobacter DIET co-culture. The discovery of a new RMIET process in Geobacter DIET co-culture suggests the complexity of IET in syntrophic bacterial communities and provides suggestions for the careful examination of the IET of other syntrophic co-cultures.
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Affiliation(s)
- Lingyan Huang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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20
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A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer. mBio 2019; 10:mBio.00789-19. [PMID: 31431545 PMCID: PMC6703419 DOI: 10.1128/mbio.00789-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The discovery of a methanogen that can conserve energy to support growth solely from the oxidation of organic carbon coupled to the reduction of an extracellular electron acceptor expands the possible environments in which methanogens might thrive. The potential importance of c-type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some Archaea was previously proposed, but these studies with Methanosarcina acetivorans provide the first genetic evidence for cytochrome-based extracellular electron transfer in Archaea. The results suggest parallels with Gram-negative bacteria, such as Shewanella and Geobacter species, in which multiheme outer-surface c-type cytochromes are an essential component for electrical communication with the extracellular environment. M. acetivorans offers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in Archaea with implications not only for methanogens but possibly also for Archaea that anaerobically oxidize methane. Extracellular electron exchange in Methanosarcina species and closely related Archaea plays an important role in the global carbon cycle and enhances the speed and stability of anaerobic digestion by facilitating efficient syntrophic interactions. Here, we grew Methanosarcina acetivorans with methanol provided as the electron donor and the humic analogue, anthraquione-2,6-disulfonate (AQDS), provided as the electron acceptor when methane production was inhibited with bromoethanesulfonate. AQDS was reduced with simultaneous methane production in the absence of bromoethanesulfonate. Transcriptomics revealed that expression of the gene for the transmembrane, multiheme, c-type cytochrome MmcA was higher in AQDS-respiring cells than in cells performing methylotrophic methanogenesis. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction but grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenzyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable the survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation of M. acetivorans makes it an excellent model microbe for evaluating c-type cytochrome-dependent extracellular electron transfer in Archaea.
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21
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Abstract
The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.
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22
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Reguera G. Microbial nanowires and electroactive biofilms. FEMS Microbiol Ecol 2019; 94:5000162. [PMID: 29931163 DOI: 10.1093/femsec/fiy086] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022] Open
Abstract
Geobacter bacteria are the only microorganisms known to produce conductive appendages or pili to electronically connect cells to extracellular electron acceptors such as iron oxide minerals and uranium. The conductive pili also promote cell-cell aggregation and the formation of electroactive biofilms. The hallmark of these electroactive biofilms is electronic heterogeneity, mediated by coordinated interactions between the conductive pili and matrix-associated cytochromes. Collectively, the matrix-associated electron carriers discharge respiratory electrons from cells in multilayered biofilms to electron-accepting surfaces such as iron oxide coatings and electrodes poised at a metabolically oxidizable potential. The presence of pilus nanowires in the electroactive biofilms also promotes the immobilization and reduction of soluble metals, even when present at toxic concentrations. This review summarizes current knowledge about the composition of the electroactive biofilm matrix and the mechanisms that allow the wired Geobacter biofilms to generate electrical currents and participate in metal redox transformations.
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Affiliation(s)
- Gemma Reguera
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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23
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Shi Z. Methylome and Metabolome Analyses Reveal Adaptive Mechanisms in Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors. J Proteome Res 2019; 18:1494-1502. [DOI: 10.1021/acs.jproteome.8b00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhenhua Shi
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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24
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Gurunathan S. Rapid biological synthesis of silver nanoparticles and their enhanced antibacterial effects against Escherichia fergusonii and Streptococcus mutans. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2014.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Kügler S, Cooper RE, Wegner CE, Mohr JF, Wichard T, Küsel K. Iron-organic matter complexes accelerate microbial iron cycling in an iron-rich fen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:972-988. [PMID: 30235650 DOI: 10.1016/j.scitotenv.2018.07.258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/09/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The accessibility of iron (Fe) species for microbial processes is dependent on solubility and redox state, which are influenced by complexation with dissolved organic matter (DOM) and water-extractable organic matter (WEOM). We evaluated the complexation of these pools of organic matter to soluble Fe(II) and Fe(III) in the slightly acidic Schlöppnerbrunnen fen and subsequent effects on Fe(II) oxidation and Fe(III) reduction. We found the majority of soluble Fe(II) and Fe(III) is complexed to DOM. High-resolution mass spectrometry identified potential complexing partners in peat-derived water extracts (PWE), including compound classes known to function as ligands or electron shuttles, like tannins and sulfur-containing compounds. Furthermore, we observed clear differences in the stability of Fe(II)- and Fe(III)-DOM, with more labile complexes dominating the upper, oxic layers (0-10 cm) and more stable complexes in lower, anoxic layers (15-30 cm). Metal isotope-coded profiling identified a single potential chemical formula (C42H57O13N9Fe2) associated with a stable Fe-DOM complex. Fe(III) reduction and Fe(II) oxidation incubations with Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1 or Sideroxydans CL-21, respectively, were used to determine the influence of Fe-DOM complexes on Fe cycling rates. The addition of PWE led to a 2.3-fold increase in Fe(III) reduction rates and 0.5-fold increase in Fe(II) oxidation rates, indicating Fe-DOM complexes greatly influence microbial Fe cycling by potentially serving as electron shuttles. Molecular analyses revealed Fe(III)-reducing and Fe(II)-oxidizing bacteria co-exist across all depths, in approximately equal proportions (representing 0.1-1.0% of the total microbial community), despite observed changes in redox potential. The activity of Fe(III)-reducing bacteria might explain the presence of the detected Fe(II) stabilized via complexation with DOM even under oxic conditions in upper peat layers. Therefore, these Fe(II)-DOM complexes can be recycled by microaerophilic Fe(II)-oxidizers. Taken together, these results suggest Fe-DOM complexation in the fen accelerates microbial-mediated redox processes across the entire redox continuum.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Jan Frieder Mohr
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany; The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany.
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Thermodynamic and functional characterization of the periplasmic triheme cytochrome PpcA from Geobacter metallireducens. Biochem J 2018; 475:2861-2875. [PMID: 30072494 DOI: 10.1042/bcj20180457] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 12/29/2022]
Abstract
The Geobacter metallireducens bacterium can couple the oxidation of a wide range of compounds to the reduction of several extracellular electron acceptors, including pollutants or electrode surfaces for current production in microbial fuel cells. For these reasons, G. metallireducens are of interest for practical biotechnological applications. The use of such electron acceptors relies on a mechanism that permits electrons to be transferred to the cell exterior. The cytochrome PpcA from G. metallireducens is a member of a family composed of five periplasmic triheme cytochromes, which are important to bridge the electron transfer from the cytoplasmic donors to the extracellular acceptors. Using NMR and visible spectroscopic techniques, a detailed thermodynamic characterization of PpcA was obtained, including the determination of the heme reduction potentials and their redox and redox-Bohr interactions. These parameters revealed unique features for PpcA from G. metallireducens compared with other triheme cytochromes from different microorganisms, namely the less negative heme reduction potentials and concomitant functional working potential ranges. It was also shown that the order of oxidation of the hemes is pH-independent, but the protein is designed to couple e-/H+ transfer exclusively at physiological pH.
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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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Teixeira LR, Dantas JM, Salgueiro CA, Cordas CM. Thermodynamic and kinetic properties of the outer membrane cytochrome OmcF, a key protein for extracellular electron transfer in Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1132-1137. [PMID: 30048624 DOI: 10.1016/j.bbabio.2018.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/17/2018] [Accepted: 07/22/2018] [Indexed: 10/28/2022]
Abstract
Gene knock-out studies on Geobacter sulfurreducens have shown that the monoheme c-type cytochrome OmcF is essential for the extracellular electron transfer pathways involved in the reduction of iron and uranium oxy-hydroxides, as well as, on electricity production in microbial fuel cells. A detailed electrochemical characterization of OmcF was performed for the first time, allowing attaining kinetics and thermodynamic data. The heterogeneous electron transfer rate constant was determined at pH 7 (0.16 ± 0.01 cm s-1) indicating that the protein displays high electron transfer efficiency compared to other monoheme cytochromes. The pH dependence of the redox potential indicates that the protein has an important redox-Bohr effect in the physiological pH range for G. sulfurreducens growth. The analysis of the structures of OmcF allowed us to assign the redox-Bohr centre to the side chain of His47 residue and its pKa values in the reduced and oxidized states were determined (pKox = 6.73; pKred = 7.55). The enthalpy, entropy and Gibbs free energy associated with the redox transaction were calculated, pointing the reduced form of the cytochrome as the most favourable. The data obtained indicate that G. sulfurreducens cells evolved to warrant a down-hill electron transfer from the periplasm to the outer-membrane associated cytochrome OmcF.
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Affiliation(s)
- Liliana R Teixeira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Joana M Dantas
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Carlos A Salgueiro
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal.
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Reguera G. Harnessing the power of microbial nanowires. Microb Biotechnol 2018; 11:979-994. [PMID: 29806247 PMCID: PMC6201914 DOI: 10.1111/1751-7915.13280] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/13/2018] [Accepted: 04/22/2018] [Indexed: 12/13/2022] Open
Abstract
The reduction of iron oxide minerals and uranium in model metal reducers in the genus Geobacter is mediated by conductive pili composed primarily of a structurally divergent pilin peptide that is otherwise recognized, processed and assembled in the inner membrane by a conserved Type IVa pilus apparatus. Electronic coupling among the peptides is promoted upon assembly, allowing the discharge of respiratory electrons at rates that greatly exceed the rates of cellular respiration. Harnessing the unique properties of these conductive appendages and their peptide building blocks in metal bioremediation will require understanding of how the pilins assemble to form a protein nanowire with specialized sites for metal immobilization. Also important are insights into how cells assemble the pili to make an electroactive matrix and grow on electrodes as biofilms that harvest electrical currents from the oxidation of waste organic substrates. Genetic engineering shows promise to modulate the properties of the peptide building blocks, protein nanowires and current‐harvesting biofilms for various applications. This minireview discusses what is known about the pilus material properties and reactions they catalyse and how this information can be harnessed in nanotechnology, bioremediation and bioenergy applications.
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Affiliation(s)
- Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd., Rm. 6190, East Lansing, MI, 48824, USA
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Costa NL, Clarke TA, Philipp LA, Gescher J, Louro RO, Paquete CM. Electron transfer process in microbial electrochemical technologies: The role of cell-surface exposed conductive proteins. BIORESOURCE TECHNOLOGY 2018; 255:308-317. [PMID: 29444758 DOI: 10.1016/j.biortech.2018.01.133] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 06/08/2023]
Abstract
Electroactive microorganisms have attracted significant interest for the development of novel biotechnological systems of low ecological footprint. These can be used for the sustainable production of energy, bioremediation of metal-contaminated environments and production of added-value products. Currently, almost 100 microorganisms from the Bacterial and Archaeal domains are considered electroactive, given their ability to efficiently interact with electrodes in microbial electrochemical technologies. Cell-surface exposed conductive proteins are key players in the electron transfer between cells and electrodes. Interestingly, it seems that among the electroactive organisms identified so far, these cell-surface proteins fall into one of four groups. In this review, the different types of cell-surface conductive proteins found in electroactive organisms will be overviewed, focusing on their structural and functional properties.
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Affiliation(s)
- Nazua L Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Laura-Alina Philipp
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany; Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal
| | - Catarina M Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal.
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Biochemical and functional insights on the triheme cytochrome PpcA from Geobacter metallireducens. Arch Biochem Biophys 2018; 644:8-16. [PMID: 29486160 DOI: 10.1016/j.abb.2018.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 02/07/2023]
Abstract
G. metallireducens bacterium has highly versatile respiratory pathways that provide the microorganism an enormous potential for many biotechnological applications. However, little is known about the structural and functional properties of its electron transfer components. In this work, the periplasmic cytochrome PpcA from G. metallireducens was studied in detail for the first time using complementary biophysical techniques, including UV-visible, CD and NMR spectroscopy. The results obtained showed that PpcA contains three low-spin c-type heme groups with His-His axial coordination, a feature also observed for its homologue in G. sulfurreducens. However, despite the high sequence homology between the two cytochromes, important structural and functional differences were observed. The comparative analysis of the backbone, side chain and heme substituents NMR signals revealed differences in the relative orientation of the hemes I and III. In addition, redox titrations followed by visible spectroscopy showed that the redox potential values for PpcA from G. metallireducens (-78 and -93 mV at pH 7 and 8, respectively) are considerably less negative. Overall, this study provides biochemical and biophysical data of a key cytochrome from G. metallireducens, paving the way to understand the extracellular electron transfer mechanisms in these bacteria.
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Ueki T, DiDonato LN, Lovley DR. Toward establishing minimum requirements for extracellular electron transfer in Geobacter sulfurreducens. FEMS Microbiol Lett 2017; 364:3796320. [PMID: 28472266 DOI: 10.1093/femsle/fnx093] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/03/2017] [Indexed: 11/12/2022] Open
Abstract
The highly redundant pathways for extracellular electron transfer in Geobacter sulfurreducens must be simplified for this microorganism to serve as an effective chassis for applications such as the development of sensors and biocomputing. Five homologs of the periplasmic c-type cytochromes, PpcA-E, offer the possibility of multiple routes of electron transfer across the periplasm. The presence of a large number of outer membrane c-type cytochromes allows G. sulfurreducens to adapt to disruption of an electron transfer pathway in the outer membrane. A strain in which genes for all five periplasmic cytochromes, PpcA-E, were deleted did not reduce Fe(III). Introducing ppcA under the control of an IPTG-inducible system in the quintuple deletion strain yielded a strain that reduced Fe(III) only in the presence of IPTG. A strain lacking known major outer membrane cytochromes, OmcB, OmcE, OmcS and OmcT, and putative functional homologs of OmcB, did not reduce Fe(III). Introduction of omcB in this septuple deletion strain restored the ability to reduce Fe(III). These results demonstrate that it is possible to trim redundancy from the extracellular electron transfer pathways in G. sulfurreducens in order to construct strains with defined extracellular electron transfer routes.
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In 't Zandt MH, Beckmann S, Rijkers R, Jetten MSM, Manefield M, Welte CU. Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well. Microb Biotechnol 2017; 11:626-638. [PMID: 28925579 PMCID: PMC6011947 DOI: 10.1111/1751-7915.12853] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/29/2022] Open
Abstract
Coal mining is responsible for 11% of total anthropogenic methane emission thereby contributing considerably to climate change. Attempts to harvest coalbed methane for energy production are challenged by relatively low methane concentrations. In this study, we investigated whether nutrient and acetate amendment of a non-producing sub-bituminous coal well could transform the system to a methane source. We tracked cell counts, methane production, acetate concentration and geochemical parameters for 25 months in one amended and one unamended coal well in Australia. Additionally, the microbial community was analysed with 16S rRNA gene amplicon sequencing at 17 and 25 months after amendment and complemented by metagenome sequencing at 25 months. We found that cell numbers increased rapidly from 3.0 × 104 cells ml-1 to 9.9 × 107 in the first 7 months after amendment. However, acetate depletion with concomitant methane production started only after 12-19 months. The microbial community was dominated by complex organic compound degraders (Anaerolineaceae, Rhodocyclaceae and Geobacter spp.), acetoclastic methanogens (Methanothrix spp.) and fungi (Agaricomycetes). Even though the microbial community had the functional potential to convert coal to methane, we observed no indication that coal was actually converted within the time frame of the study. Our results suggest that even though nutrient and acetate amendment stimulated relevant microbial species, it is not a sustainable way to transform non-producing coal wells into bioenergy factories.
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Affiliation(s)
- Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Netherlands Earth Systems Science Center, Utrecht University, Heidelberglaan 2, 3584 CS, Utrecht, The Netherlands
| | - Sabrina Beckmann
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, High Street, 2052, Sydney, NSW, Australia
| | - Ruud Rijkers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Netherlands Earth Systems Science Center, Utrecht University, Heidelberglaan 2, 3584 CS, Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike Manefield
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, High Street, 2052, Sydney, NSW, Australia
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Solution structure and dynamics of the outer membrane cytochrome OmcF from Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:733-741. [DOI: 10.1016/j.bbabio.2017.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 11/15/2022]
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Choudhury P, Prasad Uday US, Bandyopadhyay TK, Ray RN, Bhunia B. Performance improvement of microbial fuel cell (MFC) using suitable electrode and Bioengineered organisms: A review. Bioengineered 2017; 8:471-487. [PMID: 28453385 DOI: 10.1080/21655979.2016.1267883] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
There is an urgent need to find an environment friendly and sustainable technology for alternative energy due to rapid depletion of fossil fuel and industrialization. Microbial Fuel Cells (MFCs) have operational and functional advantages over the current technologies for energy generation from organic matter as it directly converts electricity from substrate at ambient temperature. However, MFCs are still unsuitable for high energy demands due to practical limitations. The overall performance of an MFC depends on microorganism, appropriate electrode materials, suitable MFC designs, and optimizing process parameters which would accelerate commercialization of this technology in near future. In this review, we put forth the recent developments on microorganism and electrode material that are critical for the generation of bioelectricity generation. This would give a comprehensive insight into the characteristics, options, modifications, and evaluations of these parameters and their effects on process development of MFCs.
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Affiliation(s)
- Payel Choudhury
- a Department of Electrical Engineering , National Institute of Technology , Agartala , India
| | | | | | - Rup Narayan Ray
- a Department of Electrical Engineering , National Institute of Technology , Agartala , India
| | - Biswanath Bhunia
- c Department of Bio Engineering , National Institute of Technology , Agartala , India
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Significance of a Posttranslational Modification of the PilA Protein of Geobacter sulfurreducens for Surface Attachment, Biofilm Formation, and Growth on Insoluble Extracellular Electron Acceptors. J Bacteriol 2017; 199:JB.00716-16. [PMID: 28138101 DOI: 10.1128/jb.00716-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/23/2017] [Indexed: 12/14/2022] Open
Abstract
Geobacter sulfurreducens, an anaerobic metal-reducing bacterium, possesses type IV pili. These pili are intrinsic structural elements in biofilm formation and, together with a number of c-type cytochromes, are thought to serve as conductive nanowires enabling long-range electron transfer (ET) to metal oxides and graphite anodes. Here, we report that a posttranslational modification of a nonconserved amino acid residue within the PilA protein, the structural subunit of the type IV pili, is crucial for growth on insoluble extracellular electron acceptors. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the secreted PilA protein revealed a posttranslational modification of tyrosine-32 with a moiety of a mass consistent with a glycerophosphate group. Mutating this tyrosine into a phenylalanine inhibited cell growth with Fe(III) oxides as the sole electron acceptor. In addition, this amino acid substitution severely diminished biofilm formation on graphite surfaces and impaired current output in microbial fuel cells. These results demonstrate that the capability to attach to insoluble electron acceptors plays a crucial role for the cells' ability to utilize them. The work suggests that glycerophosphate modification of Y32 is a key factor contributing to the surface charge of type IV pili, influencing the adhesion of Geobacter to specific surfaces.IMPORTANCE Type IV pili are bacterial appendages that function in cell adhesion, virulence, twitching motility, and long-range electron transfer (ET) from bacterial cells to insoluble extracellular electron acceptors. The mechanism and role of type IV pili for ET in Geobacter sulfurreducens is still a subject of research. In this study, we identified a posttranslational modification of the major G. sulfurreducens type IV pilin, suggested to be a glycerophosphate moiety. We show that a mutant in which the glycerophosphate-modified tyrosine-32 is replaced with a phenylalanine has reduced abilities for ET and biofilm formation compared with those of the wild type. The results show the importance of the glycerophosphate-modified tyrosine for surface attachment and electron transfer in electrode- or Fe(III)-respiring G. sulfurreducens cells.
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Speers AM, Schindler BD, Hwang J, Genc A, Reguera G. Genetic Identification of a PilT Motor in Geobacter sulfurreducens Reveals a Role for Pilus Retraction in Extracellular Electron Transfer. Front Microbiol 2016; 7:1578. [PMID: 27799920 PMCID: PMC5065972 DOI: 10.3389/fmicb.2016.01578] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/21/2016] [Indexed: 12/13/2022] Open
Abstract
The metal-reducing bacterium Geobacter sulfurreducens requires the expression of conductive pili to reduce iron oxides and to wire electroactive biofilms, but the role of pilus retraction in these functions has remained elusive. Here we show that of the four PilT proteins encoded in the genome of G. sulfurreducens, PilT3 powered pilus retraction in planktonic cells of a PilT-deficient strain of P. aeruginosa and restored the dense mutant biofilms to wild-type levels. Furthermore, PilT3 and PilT4 rescued the twitching motility defect of the PilT-deficient mutant. However, PilT4 was the only paralog whose inactivation in G. sulfurreducens lead to phenotypes associated with the hyperpiliation of non-retractile mutants such as enhanced adhesion and biofilm-forming abilities. In addition, PilT4 was required to reduce iron oxides. Taken together, the results indicate that PilT4 is the motor ATPase of G. sulfurreducens pili and reveal a previously unrecognized role for pilus retraction in extracellular electron transfer, a strategy that confers on Geobacter spp. an adaptive advantage for metal reduction in the natural environment.
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Affiliation(s)
- Allison M Speers
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Bryan D Schindler
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Jihwan Hwang
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Aycin Genc
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
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Steidl RJ, Lampa-Pastirk S, Reguera G. Mechanistic stratification in electroactive biofilms of Geobacter sulfurreducens mediated by pilus nanowires. Nat Commun 2016; 7:12217. [PMID: 27481214 PMCID: PMC4974642 DOI: 10.1038/ncomms12217] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/09/2016] [Indexed: 01/08/2023] Open
Abstract
Electricity generation by Geobacter sulfurreducens biofilms grown on electrodes involves matrix-associated electron carriers, such as c-type cytochromes. Yet, the contribution of the biofilm's conductive pili remains uncertain, largely because pili-defective mutants also have cytochrome defects. Here we report that a pili-deficient mutant carrying an inactivating mutation in the pilus assembly motor PilB has no measurable defects in cytochrome expression, yet forms anode biofilms with reduced electroactivity and is unable to grow beyond a threshold distance (∼10 μm) from the underlying electrode. The defects are similar to those of a Tyr3 mutant, which produces poorly conductive pili. The results support a model in which the conductive pili permeate the biofilms to wire the cells to the conductive biofilm matrix and the underlying electrode, operating coordinately with cytochromes until the biofilm reaches a threshold thickness that limits the efficiency of the cytochrome pathway but not the functioning of the conductive pili network. The roles played by cytochromes and conductive filamentous appendages (pili) in the electrical conductivity of Geobacter bacterial biofilms are controversial. Here, Steidl et al. present evidence that both mechanisms cooperate in thin biofilms, while pili are important for conductivity across thicker biofilms.
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Affiliation(s)
- Rebecca J Steidl
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, Rm 6190, Biomedical and Physical Science building, East Lansing, Michigan 48824, USA
| | - Sanela Lampa-Pastirk
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, Rm 6190, Biomedical and Physical Science building, East Lansing, Michigan 48824, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, Rm 6190, Biomedical and Physical Science building, East Lansing, Michigan 48824, USA
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Santos TC, Silva MA, Morgado L, Dantas JM, Salgueiro CA. Diving into the redox properties of Geobacter sulfurreducens cytochromes: a model for extracellular electron transfer. Dalton Trans 2016; 44:9335-44. [PMID: 25906375 DOI: 10.1039/c5dt00556f] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Geobacter bacteria have a remarkable respiratory versatility that includes the dissimilatory reduction of insoluble metal oxides in natural habitats and electron transfer to electrode surfaces from which electricity can be harvested. In both cases, electrons need to be exported from the cell interior to the exterior via a mechanism designated as extracellular electron transfer (EET). Several c-type cytochromes from G. sulfurreducens (Gs) were identified as key players in this process. Biochemical and biophysical data have been obtained for ten Gs cytochromes, including inner-membrane associated (MacA), periplasmic (PpcA, PpcB, PpcC, PpcD, PpcE and GSU1996) and outer membrane-associated (OmcF, OmcS and OmcZ). The redox properties of these cytochromes have been determined, except for PpcC and GSU1996. In this perspective, the reduction potentials of these two cytochromes were determined by potentiometric redox titrations followed by visible spectroscopy. The data obtained are taken together with those available for other key cytochromes to present a thorough overview of the current knowledge of Gs EET mechanisms and provide a possible rationalization for the existence of several multiheme cytochromes involved in the same respiratory pathways.
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Affiliation(s)
- Telma C Santos
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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Unraveling the electron transfer processes of a nanowire protein from Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:7-13. [DOI: 10.1016/j.bbabio.2015.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/04/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022]
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Feliciano GT, Steidl RJ, Reguera G. Structural and functional insights into the conductive pili of Geobacter sulfurreducens revealed in molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:22217-26. [PMID: 26243427 DOI: 10.1039/c5cp03432a] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Geobacter sulfurreducens (GS) electronically connects with extracellular electron acceptors using conductive protein filaments or pili. To gain insights into their role as biological nanowires, we investigated the structural dynamics of the GS pilus in solution via molecular dynamics simulations. In the model, all of the pilin's aromatics clustered as a right-handed helical band along the pilus, maintaining inter-aromatic distances and dimer configurations optimal for multistep hopping. The aromatics were interspersed within the regions of highest negative potential, which influenced the type and configuration of the aromatic contacts and the rates of electron transfer. Small foci of positive potential were also present but were neutralized within uncharged regions, thus minimizing charge trapping. Consistent with the model predictions, mutant strains with reduced aromatic contacts or negative potentials had defects in pili functions such as the reduction of Fe(III) oxides and electrodes. The results therefore support the notion of a pilus fiber evolved to function as an electronic conduit between the cell and extracellular electron acceptors.
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Affiliation(s)
- G T Feliciano
- Departamento de Físico-Química, Instituto de Quimica, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Nanobionics Group, Sao Paulo, Araraquara, Brazil
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Dantas JM, Morgado L, Aklujkar M, Bruix M, Londer YY, Schiffer M, Pokkuluri PR, Salgueiro CA. Rational engineering of Geobacter sulfurreducens electron transfer components: a foundation for building improved Geobacter-based bioelectrochemical technologies. Front Microbiol 2015; 6:752. [PMID: 26284042 PMCID: PMC4519760 DOI: 10.3389/fmicb.2015.00752] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022] Open
Abstract
Multiheme cytochromes have been implicated in Geobacter sulfurreducens extracellular electron transfer (EET). These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by G. sulfurreducens. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Over the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of G. sulfurreducens multiheme cytochromes and also to identify key residues in these proteins for EET. In previous studies, we set the foundations for enhancement of the EET abilities of G. sulfurreducens by characterizing a family of five triheme cytochromes (PpcA-E). These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell's outer surface. The results obtained suggested that PpcA can couple e−/H+ transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e−/H+ transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of G. sulfurreducens. For the first time G. sulfurreducens strains have been manipulated by the introduction of mutant forms of essential proteins with the aim to develop and improve bioelectrochemical technologies.
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Affiliation(s)
- Joana M Dantas
- Research Unit on Applied Molecular Biosciences (UCIBIO), Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Caparica, Portugal
| | - Leonor Morgado
- Research Unit on Applied Molecular Biosciences (UCIBIO), Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Caparica, Portugal
| | - Muktak Aklujkar
- Department of Biological Sciences, Towson University Towson, MD, USA
| | - Marta Bruix
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Yuri Y Londer
- Biosciences Division, Argonne National Laboratory Lemont, IL, USA
| | | | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory Lemont, IL, USA
| | - Carlos A Salgueiro
- Research Unit on Applied Molecular Biosciences (UCIBIO), Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Caparica, Portugal
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Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer SW, Smith RD, Lipton MS. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis. J Proteome Res 2015; 14:1361-75. [PMID: 25496566 DOI: 10.1021/pr500983v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Bacterial extracellular metal respiration, as carried out by members of the genus Geobacter, is of interest for applications including microbial fuel cells and bioremediation. Geobacter bemidjiensis is the major species whose growth is stimulated during groundwater amendment with acetate. We have carried out label-free proteomics studies of G. bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate, or one of two hydrous ferric oxide mineral types as electron acceptor. The major class of proteins whose expression changes across these conditions is c-type cytochromes, many of which are known to be involved in extracellular metal reduction in other, better-characterized Geobacter species. Some proteins with multiple homologues in G. bemidjiensis (OmcS, OmcB) had different expression patterns than observed for their G. sulfurreducens homologues under similar growth conditions. We also compared the proteome from our study to a prior proteomics study of biomass recovered from an aquifer in Colorado, where the microbial community was dominated by strains closely related to G. bemidjiensis. We detected an increased number of proteins with functions related to motility and chemotaxis in the Colorado field samples compared to the laboratory samples, suggesting the importance of motility for in situ extracellular metal respiration.
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Affiliation(s)
- Eric D Merkley
- Signature Sciences and Technology Division, and ‡Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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Electroactive bacteria—molecular mechanisms and genetic tools. Appl Microbiol Biotechnol 2014; 98:8481-95. [DOI: 10.1007/s00253-014-6005-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
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Abundance of the multiheme c-type cytochrome OmcB increases in outer biofilm layers of electrode-grown Geobacter sulfurreducens. PLoS One 2014; 9:e104336. [PMID: 25090411 PMCID: PMC4121341 DOI: 10.1371/journal.pone.0104336] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/14/2014] [Indexed: 11/25/2022] Open
Abstract
When Geobacter sulfurreducens utilizes an electrode as its electron acceptor, cells embed themselves in a conductive biofilm tens of microns thick. While environmental conditions such as pH or redox potential have been shown to change close to the electrode, less is known about the response of G. sulfurreducens to growth in this biofilm environment. To investigate whether respiratory protein abundance varies with distance from the electrode, antibodies against an outer membrane multiheme cytochrome (OmcB) and cytoplasmic acetate kinase (AckA) were used to determine protein localization in slices spanning ∼25 µm-thick G. sulfurreducens biofilms growing on polished electrodes poised at +0.24 V (vs. Standard Hydrogen Electrode). Slices were immunogold labeled post-fixing, imaged via transmission electron microscopy, and digitally reassembled to create continuous images allowing subcellular location and abundance per cell to be quantified across an entire biofilm. OmcB was predominantly localized on cell membranes, and 3.6-fold more OmcB was detected on cells 10–20 µm distant from the electrode surface compared to inner layers (0–10 µm). In contrast, acetate kinase remained constant throughout the biofilm, and was always associated with the cell interior. This method for detecting proteins in intact conductive biofilms supports a model where the utilization of redox proteins changes with depth.
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Zhang T, Tremblay PL, Chaurasia AK, Smith JA, Bain TS, Lovley DR. Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens. Front Microbiol 2014; 5:245. [PMID: 24904558 PMCID: PMC4033198 DOI: 10.3389/fmicb.2014.00245] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/05/2014] [Indexed: 11/13/2022] Open
Abstract
Although the biochemical pathways for the anaerobic degradation of many of the hydrocarbon constituents in petroleum reservoirs have been elucidated, the mechanisms for anaerobic activation of benzene, a very stable molecule, are not known. Previous studies have demonstrated that Geobacter metallireducens can anaerobically oxidize benzene to carbon dioxide with Fe(III) as the sole electron acceptor and that phenol is an intermediate in benzene oxidation. In an attempt to identify enzymes that might be involved in the conversion of benzene to phenol, whole-genome gene transcript abundance was compared in cells metabolizing benzene and cells metabolizing phenol. Eleven genes had significantly higher transcript abundance in benzene-metabolizing cells. Five of these genes had annotations suggesting that they did not encode proteins that could be involved in benzene metabolism and were not further studied. Strains were constructed in which one of the remaining six genes was deleted. The strain in which the monocistronic gene Gmet 0232 was deleted metabolized phenol, but not benzene. Transcript abundance of the adjacent monocistronic gene, Gmet 0231, predicted to encode a zinc-containing oxidoreductase, was elevated in cells metabolizing benzene, although not at a statistically significant level. However, deleting Gmet 0231 also yielded a strain that could metabolize phenol, but not benzene. Although homologs of Gmet 0231 and Gmet 0232 are found in microorganisms not known to anaerobically metabolize benzene, the adjacent localization of these genes is unique to G. metallireducens. The discovery of genes that are specifically required for the metabolism of benzene, but not phenol in G. metallireducens is an important step in potentially identifying the mechanisms for anaerobic benzene activation.
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Affiliation(s)
- Tian Zhang
- Department of Microbiology, University of Massachusetts Amherst, MA, USA ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark
| | - Pier-Luc Tremblay
- Department of Microbiology, University of Massachusetts Amherst, MA, USA ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark
| | | | - Jessica A Smith
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Timothy S Bain
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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Going wireless: Fe(III) oxide reduction without pili by Geobacter sulfurreducens strain JS-1. Appl Environ Microbiol 2014; 80:4331-40. [PMID: 24814783 DOI: 10.1128/aem.01122-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have suggested that the conductive pili of Geobacter sulfurreducens are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of G. sulfurreducens reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (>30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the c-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through G. sulfurreducens biofilms is more effective via pili.
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Anaerobic benzene oxidation via phenol in Geobacter metallireducens. Appl Environ Microbiol 2013; 79:7800-6. [PMID: 24096430 DOI: 10.1128/aem.03134-13] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated in Geobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (<0.5 μM) of phenol accumulated in cultures of Geobacter metallireducens anaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures of Geobacter sulfurreducens, a Geobacter species that cannot metabolize benzene. The phenol produced in G. metallireducens cultures was labeled with (18)O during growth in H2(18)O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in which Geobacter species are considered to play an important role in anaerobic benzene degradation.
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A long way to the electrode: how do Geobacter cells transport their electrons? Biochem Soc Trans 2013; 40:1274-9. [PMID: 23176467 DOI: 10.1042/bst20120046] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mechanism of electron transport in Geobacter sulfurreducens biofilms is a topic under intense study and debate. Although some proteins were found to be essential for current production, the specific role that each one plays in electron transport to the electrode remains to be elucidated and a consensus on the mechanism of electron transport has not been reached. In the present paper, to understand the state of the art in the topic, electron transport from inside of the cell to the electrode in Geobacter sulfurreducens biofilms is analysed, reviewing genetic studies, biofilm conductivity assays and electrochemical and spectro-electrochemical experiments. Furthermore, crucial data still required to achieve a deeper understanding are highlighted.
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Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:484-92. [DOI: 10.1016/j.bbabio.2012.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/11/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
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