1
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Klein E, Wurst R, Rehnlund D, Gescher J. Elucidating the development of cooperative anode-biofilm-structures. Biofilm 2024; 7:100193. [PMID: 38601817 PMCID: PMC11004076 DOI: 10.1016/j.bioflm.2024.100193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024] Open
Abstract
Microbial electrochemical systems are a highly versatile platform technology with a particular focus on the interplay of chemical and electrical energy conversion and offer immense potential for a sustainable bioeconomy. The industrial realization of this potential requires a critical focus on biofilm optimization if performance is to be controlled over a long period of time. Moreover, the aspect and influence of cooperativity has to be addressed as many applied anodic bioelectrochemical systems will most likely be operated with a diversity of interacting microbial species. Hence, the aim of this study was to analyze how interspecies dependence and cooperativity of a model community influence the development of anodic biofilms. To investigate biofilm activity in a spatially resolved manner, a microfluidic bioelectrochemical flow cell was developed that can be equipped with user-defined electrode materials and operates under laminar flow conditions. With this infrastructure, the development of single and co-culture biofilms of the two model organisms Shewanella oneidensis and Geobacter sulfurreducens on graphite electrodes was monitored by optical coherence tomography analysis. The interdependence in the co-culture biofilm was achieved by feeding the community with lactate, which is converted by S. oneidensis into acetate, which in turn serves as substrate for G. sulfurreducens. The results show that co-cultivation resulted in the formation of denser biofilms than in single culture. Moreover, we hypothesize that S. oneidensis in return utilizes the conductive biofilm matrix build by G. sulfurreducens for direct interspecies electron transfer (DIET) to the anode. FISH analysis revealed that the biofilms consisted of approximately two-thirds G. sulfurreducens cells, which most likely formed a conductive 3D network throughout the biofilm matrix, in which evenly distributed tubular S. oneidensis colonies were embedded without direct contact to the anode surface. Live/dead staining shows that the outermost biofilm contained almost exclusively dead cells (98 %), layers near the anode contained 45-56 % and the entire biofilm contained 82 % live cells. Our results exemplify how the architecture of the exoelectrogenic biofilm dynamically adapts to the respective process conditions.
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Affiliation(s)
- Edina Klein
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
| | - René Wurst
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
| | - David Rehnlund
- Department of Chemistry – Ångström Laboratory, Uppsala University, Box 538, SE-751 21, Uppsala, Sweden
| | - Johannes Gescher
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
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2
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Lin T, Ding W, Zhang D, You Z, Yang Y, Li F, Xu D, Lovley DR, Song H. Expression of filaments of the Geobacter extracellular cytochrome OmcS in Shewanella oneidensis. Biotechnol Bioeng 2024; 121:2002-2012. [PMID: 38555482 DOI: 10.1002/bit.28702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
The physiological role of Geobacter sulfurreducens extracellular cytochrome filaments is a matter of debate and the development of proposed electronic device applications of cytochrome filaments awaits methods for large-scale cytochrome nanowire production. Functional studies in G. sulfurreducens are stymied by the broad diversity of redox-active proteins on the outer cell surface and the redundancy and plasticity of extracellular electron transport routes. G. sulfurreducens is a poor chassis for producing cytochrome nanowires for electronics because of its slow, low-yield, anaerobic growth. Here we report that filaments of the G. sulfurreducens cytochrome OmcS can be heterologously expressed in Shewanella oneidensis. Multiple lines of evidence demonstrated that a strain of S. oneidensis, expressing the G. sulfurreducens OmcS gene on a plasmid, localized OmcS on the outer cell surface. Atomic force microscopy revealed filaments with the unique morphology of OmcS filaments emanating from cells. Electron transfer to OmcS appeared to require a functional outer-membrane porin-cytochrome conduit. The results suggest that S. oneidensis, which grows rapidly to high culture densities under aerobic conditions, may be suitable for the development of a chassis for producing cytochrome nanowires for electronics applications and may also be a good model microbe for elucidating cytochrome filament function in anaerobic extracellular electron transfer.
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Affiliation(s)
- Tong Lin
- Frontiers Science Centre for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- College of Life Science, Langfang Normal University, Langfang, Hebei, China
| | - Wenqi Ding
- Frontiers Science Centre for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Danni Zhang
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Zixuan You
- Frontiers Science Centre for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yun Yang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, China
| | - Feng Li
- Frontiers Science Centre for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Derek R Lovley
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Hao Song
- Frontiers Science Centre for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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3
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Liu C, Guo D, Wen S, Dang Y, Sun D, Li P. Transcriptomic insights unveil the crucial roles of cytochromes, NADH, and pili in Ag(I) reduction by Geobacter sulfurreducens. CHEMOSPHERE 2024; 358:142174. [PMID: 38685325 DOI: 10.1016/j.chemosphere.2024.142174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/03/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Silver (Ag) is a pivotal transition metal with applications in multiple industries, necessitating efficient recovery techniques. Despite various proposed methods for silver recovery from wastewaters, challenges persist especially for low concentrations. In this context, bioreduction by bacteria like Geobacter sulfurreducens, offers a promising approach by converting Ag(I) to Ag nanoparticles. To reveal the mechanisms driving microbial Ag(I) reduction, we conducted transcriptional profiling of G. sulfurreducens under Ag(I)-reducing condition. Integrated transcriptomic and protein-protein interaction network analyses identified significant transcriptional shifts, predominantly linked to c-type cytochromes, NADH, and pili. When compared to a pilus-deficient strain, the wild-type strain exhibited distinct cytochrome gene expressions, implying specialized functional roles. Additionally, despite a down-regulation in NADH dehydrogenase genes, we observed up-regulation of specific downstream cytochrome genes, highlighting NADH's potential role as an electron donor in the Ag(I) reduction process. Intriguingly, our findings also highlight the significant influence of pili on the morphology of the resulting Ag nanoparticles. The presence of pili led to the formation of smaller and more crystallized Ag nanoparticles. Overall, our findings underscore the intricate interplay of cytochromes, NADH, and pili in Ag(I) reduction. Such insights suggest potential strategies for further enhancing microbial Ag(I) reduction.
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Affiliation(s)
- Chunmao Liu
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Dongchao Guo
- School of Computer Science, Beijing Information Science and Technology University, Beijing, 100101, China
| | - Su Wen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yan Dang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Dezhi Sun
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Pengsong Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
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4
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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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5
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Schwarz IA, Alsaqri B, Lekbach Y, Henry K, Gorman S, Woodard T, Dion L, Real L, Holmes DE, Smith JA, Lovley DR. Lack of physiological evidence for cytochrome filaments functioning as conduits for extracellular electron transfer. mBio 2024; 15:e0069024. [PMID: 38717196 PMCID: PMC11077965 DOI: 10.1128/mbio.00690-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/12/2024] Open
Abstract
Extracellular cytochrome filaments are proposed to serve as conduits for long-range extracellular electron transfer. The primary functional physiological evidence has been the reported inhibition of Geobacter sulfurreducens Fe(III) oxide reduction when the gene for the filament-forming cytochrome OmcS is deleted. Here we report that the OmcS-deficient strain from that original report reduces Fe(III) oxide as well as the wild-type, as does a triple mutant in which the genes for the other known filament-forming cytochromes were also deleted. The triple cytochrome mutant displayed filaments with the same 3 nm diameter morphology and conductance as those produced by Escherichia coli heterologously expressing the G. sulfurreducens PilA pilin gene. Fe(III) oxide reduction was inhibited when the pilin gene in cytochrome-deficient mutants was modified to yield poorly conductive 3 nm diameter filaments. The results are consistent with the concept that 3 nm diameter electrically conductive pili (e-pili) are required for G. sulfurreducens long-range extracellular electron transfer. In contrast, rigorous physiological functional evidence is lacking for cytochrome filaments serving as conduits for long-range electron transport. IMPORTANCE Unraveling microbial extracellular electron transfer mechanisms has profound implications for environmental processes and advancing biological applications. This study on Geobacter sulfurreducens challenges prevailing beliefs on cytochrome filaments as crucial components thought to facilitate long-range electron transport. The discovery of an OmcS-deficient strain's unexpected effectiveness in Fe(III) oxide reduction prompted a reevaluation of the key conduits for extracellular electron transfer. By exploring the impact of genetic modifications on G. sulfurreducens' performance, this research sheds light on the importance of 3-nm diameter electrically conductive pili in Fe(III) oxide reduction. Reassessing these mechanisms is essential for uncovering the true drivers of extracellular electron transfer in microbial systems, offering insights that could revolutionize applications across diverse fields.
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Affiliation(s)
- Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Baha Alsaqri
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Yassir Lekbach
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Kathryn Henry
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Sydney Gorman
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor Woodard
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Laura Dion
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Lauren Real
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Jessica A. Smith
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Zhuang X, Wang S, Wu S. Electron Transfer in the Biogeochemical Sulfur Cycle. Life (Basel) 2024; 14:591. [PMID: 38792612 PMCID: PMC11123123 DOI: 10.3390/life14050591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability to perform extracellular electron transfer. A growing body of research has highlighted their extensive phylogenetic and metabolic diversity, revealing their crucial roles in ecological processes. In this review, we delve into the electron transfer process between sulfate-reducing bacteria and anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, we review the phenomenon of long-distance electron transfer and potential extracellular electron transfer in multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with their vast application prospects and ecological significance, play a pivotal role in various ecological processes. Subsequently, we discuss the important role of the pili/cytochrome for electron transfer and presented cutting-edge approaches for exploring and studying electroactive microorganisms. This review provides a comprehensive overview of electroactive microorganisms participating in the biogeochemical sulfur cycle. By examining their electron transfer mechanisms, and the potential ecological and applied implications, we offer novel insights into microbial sulfur metabolism, thereby advancing applications in the development of sustainable bioelectronics materials and bioremediation technologies.
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Affiliation(s)
- Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.Z.); (S.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.Z.); (S.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.Z.); (S.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Guberman-Pfeffer MJ. To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'. Front Microbiol 2024; 15:1397124. [PMID: 38633696 PMCID: PMC11021709 DOI: 10.3389/fmicb.2024.1397124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.
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Xu D, Ando N. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. J Struct Biol 2024; 216:108072. [PMID: 38431179 DOI: 10.1016/j.jsb.2024.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/11/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
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Affiliation(s)
- Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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9
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Xu D, Ando N. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.08.570849. [PMID: 38405773 PMCID: PMC10888874 DOI: 10.1101/2023.12.08.570849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
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Affiliation(s)
- Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
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10
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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11
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Carducci NGG, Dey S, Hickey DP. Recent Developments and Applications of Microbial Electrochemical Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024. [PMID: 38273205 DOI: 10.1007/10_2023_236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
This chapter provides a comprehensive overview of microbial electrochemical biosensors, which are a unique class of biosensors that utilize the metabolic activity of microorganisms to convert chemical signals into electrical signals. The principles and mechanisms of these biosensors are discussed, including the different types of microorganisms that can be used. The various applications of microbial electrochemical biosensors in fields such as environmental monitoring, medical diagnostics, and food safety are also explored. The chapter concludes with a discussion of future research directions and potential advancements in the field of microbial electrochemical biosensors.
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Affiliation(s)
- Nunzio Giorgio G Carducci
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Sunanda Dey
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - David P Hickey
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
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Liu Y, Xu L, Su J, Ali A, Huang T, Wang Y, Zhang P. Microbially driven Fe-N cycle: Intrinsic mechanisms, enhancement, and perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168084. [PMID: 37924885 DOI: 10.1016/j.scitotenv.2023.168084] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/21/2023] [Accepted: 10/21/2023] [Indexed: 11/06/2023]
Abstract
The iron‑nitrogen (FeN) cycle driven by microbes has great potential for treating wastewater. Fe is a metal that is frequently present in the environment and one of the crucial trace elements needed by microbes. Due to its synergistic role in the microbial N removal process, Fe goes much beyond the essential nutritional needs of microorganisms. Investigating the mechanisms behind the linked Fe-N cycle driven by microbes is crucial. The Fe-N cycle is frequently connected with anaerobic ammonia oxidation (anammox), nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), Feammox, and simultaneous nitrification denitrification (SND), etc. Although the main mechanisms of Fe-mediated biological N removal may vary depending on the valence state of the Fe, their similar transformation pathways may provide information on the study of certain element-microbial interactions. This review offers a thorough analysis of the facilitation effect and influence of Fe on the removal of nitrogenous pollutants in various biological N removal processes and summarizes the ideal Fe dosing. Additionally, the synergistic mechanisms of Fe and microbial synergistic N removal process are elaborated, covering four aspects: enzyme activity, electron transfer, microbial extracellular polymeric substances (EPS) secretion, and microbial community interactions. The methods to improve biological N removal based on the intrinsic mechanism were also discussed, with the aim of thoroughly understanding the biological mechanisms of Fe in the microbial N removal process and providing a reference and thinking for employing Fe to promote microbial N removal in practical applications.
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Affiliation(s)
- Yan Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Liang Xu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Junfeng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Amjad Ali
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Peng Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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Xia R, Cheng J, Chen Z, Zhang Z, Zhou X, Zhou J. Co-NC@Co-NP hierarchical nanoforest steering charge exchange efficiency at biotic-abiotic interface for microbial electrochemical carbon reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166793. [PMID: 37666340 DOI: 10.1016/j.scitotenv.2023.166793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Converting anthropogenic carbon dioxide (CO2) to value-added products using bio-electrochemical conversions represents a promising strategy for producing sustainable fuel. However, the reaction kinetics are hindered by insufficient attachment of microorganisms and limited charge extraction at the bioinorganic interface. A hierarchical nanoforest with doped cobalt‑nitrogen-doped carbon covering cobalt nanoparticle (Co-NC@Co-NP) was integrated with a CO2-to-CH4 conversion microbiome for methane production to address these shortcomings. In-situ nanoforests were developed on the nanosheet by chemical vapor deposition with Co nanoparticles catalyzed. The bio-nanowire-like carbon nanotubes enhanced the electrostatic force for microbe enrichment via the tip effect, providing a maximum of 3.6-fold electron-receiving microbes to utilize reducing equivalents. The Co-NC@Co-NP enhanced the direct electron transfer between microbes and electrodes, reducing the adoption of energy barriers for heme-like proteins. Thus, the optimized electron transfer pathway improved selectivity by a factor of 2.0 compared to the pristine nanosheet biohybrid. Furthermore, the adjusted microbial community structure provided sufficient methanogenesis genes to match the strong electron flow, achieving maximal methane production rates (311.1 mmol/m2/day at -0.9 V vs. Ag/AgCl), 8.62 times higher than those of the counterpart nanosheet biohybrid (36.06 mmol/m2/day). This work demonstrates a comprehensive assessment of biotic-abiotic energy transfer, which may serve as a guiding principle for designing efficient bio-electrochemical systems.
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Affiliation(s)
- Rongxin Xia
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Jun Cheng
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China; Key Laboratory of Low-grade Energy Utilization Technologies and Systems of Ministry of Education, Chongqing University, Chongqing 400044, China.
| | - Zhuo Chen
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Ze Zhang
- Shanghai Institute of Space Propulsion, Shanghai 201112, China; Shanghai Academy of Spaceflight Technology (SAST), Shanghai 201109, China
| | - Xinyi Zhou
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Junhu Zhou
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
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Xia R, Cheng J, Chen Z, Zhang Z, Zhou X, Zhou J, Zhang M. Revealing Co-N 4 @Co-NP Bridge-Enabled Fast Charge Transfer and Active Intracellular Methanogenesis in Bio-Electrochemical CO 2 -Conversion with Methanosarcina Barkeri. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304920. [PMID: 37689983 DOI: 10.1002/adma.202304920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/05/2023] [Indexed: 09/11/2023]
Abstract
To significantly advance the bio-electrochemical CO2 -conversion rate and unfold the correlation between the abiotic electrode and the attached microorganisms, an atomic-nanoparticle bridge of Co-N4 @Co-NP crafted in metal-organic frameworks-derived nanosheets is integrated with a model methanogen of Methanosarcina barkeri (M. barkeri). The direct bonding of N in Co-N4 and Fe in member protein of Cytochrome b (Cytb) activates a fast direct electron transfer path while the Co nanoparticles further strengthen this bonding via decreasing the energy gap between the p-band center of N and the d-band center of Fe. This multiorbital tuning operation of Co nanoparticles also enhances the coenzyme F420-mediated electron transfer by enabling the electron flow direct to the hydrogenation sites. Particularly, the increased surface electric field of the Co-N4 @Co-NP bridge-based nanosheet electrode facilitates the interfacial Na+ accumulation to expedite ATPase transport for powering intracellular CO2 conversion. Remarkably, the self-assembled M.barkeri-Co-N4 @Co-NP biohybrid achieves a high methane production rate of 3860 mmol m-2 day-1 , which greatly outperforms other reported biohybrid systems. This work demonstrates a comprehensive scrutinization of biotic-abiotic energy transfer, which may serve as a guiding principle for efficient bio-electrochemical system design.
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Affiliation(s)
- Rongxin Xia
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Jun Cheng
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
- Key Laboratory of Low-Grade Energy Utilization Technologies and Systems of Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Zhuo Chen
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Ze Zhang
- Shanghai Institute of Space Propulsion, Shanghai, 201112, China
- Shanghai Academy of Spaceflight Technology (SAST), Shanghai, 201109, China
| | - Xinyi Zhou
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Junhu Zhou
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Meng Zhang
- State Key Laboratory for Extreme Photonics and Instrumentation, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, 310027, China
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15
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Zhou H, Xuanyuan X, Lv X, Wang J, Feng K, Chen C, Ma J, Xing D. Mechanisms of magnetic sensing and regulating extracellular electron transfer of electroactive bacteria under magnetic fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165104. [PMID: 37356761 DOI: 10.1016/j.scitotenv.2023.165104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/05/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Electroactive bacteria can display notable plasticity in their response to magnetic field (MF), which prompted bioelectrochemical system as promising candidates for magnetic sensor applications. In this study, we explored the sensing and stimulatory effect of MF on current generation by Geobacter sulfurreducens, and elucidated the related molecular mechanism at the transcriptomic level. MF treatment significantly enhanced electricity generation and overall energy efficiency of G. sulfurreducens by 50 % and 22 %, respectively. The response of current to MFs was instantaneous and reversible. Cyclic voltammetry analysis of the anode biofilm revealed that the redox couples changed from -0.31 to -0.39 V (vs. Ag/AgCl), suggesting that MFs could alter electron transfer related components. Differential gene expression analysis further verified this hypothesis, genes associated with electron transfer were upregulated in G. sulfurreducens under MF treatment relative to the control group, specifically, genes encoding periplasmic c-type cytochromes (ppcA and ppcD), outer membrane cytochrome (omcF, omcZ, omcB), pili (pilA-C, pilM, and pilV2), and ribosome. The enhanced bacterial extracellular electron transfer process was also linked to the overexpression of the NADH dehydrogenase I subunit, the ABC transporter, transcriptional regulation, and ATP synthase. Overall, our findings shed light on the molecular mechanism underlying the effects of magnetic field stimuli on EAB and provide a theoretical basis for its further application in magnetic sensors and other biological system.
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Affiliation(s)
- Huihui Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Xianwen Xuanyuan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Xiaowei Lv
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Jing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Kun Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China.
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16
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Jiang J, He P, Luo Y, Peng Z, Jiang Y, Hu Y, Qi L, Dong X, Dong Y, Shi L. The varied roles of pilA-N, omcE, omcS, omcT, and omcZ in extracellular electron transfer by Geobacter sulfurreducens. Front Microbiol 2023; 14:1251346. [PMID: 37881251 PMCID: PMC10597711 DOI: 10.3389/fmicb.2023.1251346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
Geobacter sulfurreducens mediates extracellular electron transfer (EET) reactions with different substrates, such as solid-phase Fe(III)-containing minerals, anodes and the cells of Geobacter metallireducens. To compare their roles in EET, the pilA-N, omcE, omcS, omcT and omcZ genes of G. sulfurreducens were systematically deleted. All mutants showed impaired and varied ability to form biofilms on nonconductive surface. Deletion of omcE also impaired bacterial ability to reduce ferrihydrite, but its impacts on the ability for anode reduction and the co-culture of G. metallireducens-G. sulfurreducens were minimal. The mutant without omcS showed diminished ability to reduce ferrihydrite and to form the co-culture, but was able to regain its ability to reduce anodes. Deletion of omcT, omcZ or pilA-N alone impaired bacterial ability to reduce ferrihydrite and anodes and to form the co-culture. Deletion of all tested genes abolished bacterial ability to reduce ferrihydrite and anodes. Triple-deletion of all omcS, omcT and omcZ abolished the ability of G. sulfurreducens to co-culture with G. metallireducens. However, deletion of only omcZ or pilA-N or both omcS and omcT abolished the ability of G. sulfurreducens without hydrogenase gene hybL to co-culture with G. metallireducens, which show their indispensable roles in direct electron transfer from G. metallireducens to G. sulfurreducens. Thus, the roles of pilA-N, omcE, omcS, omcT and omcZ for G. sulfurreducens in EET vary substantially, which also suggest that possession of PilA-N and multiple cytochromes of different structures enables G. sulfurreducens to mediate EET reactions efficiently with substrates of different properties.
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Affiliation(s)
- Jie Jiang
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
| | - Pengchen He
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
| | - Ying Luo
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
| | - Zhaofeng Peng
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
| | - Yongguang Jiang
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
| | - Yidan Hu
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences-Wuhan, Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences-Wuhan, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences-Wuhan, Wuhan, China
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences-Wuhan, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences-Wuhan, Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences-Wuhan, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences-Wuhan, Wuhan, China
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17
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Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
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Affiliation(s)
- Jeanine S. Geelhoed
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
| | - Casper A. Thorup
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Filip J. R. Meysman
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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18
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Gralnick JA, Bond DR. Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest. Annu Rev Microbiol 2023; 77:517-539. [PMID: 37713456 DOI: 10.1146/annurev-micro-032221-023725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
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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19
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Guberman-Pfeffer MJ. Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires. J Phys Chem B 2023; 127:7148-7161. [PMID: 37552847 DOI: 10.1021/acs.jpcb.3c02912] [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] [Indexed: 08/10/2023]
Abstract
Structural determinants of a 103-fold variation in electrical conductivity for helical homopolymers of tetra-, hexa-, and octa-heme cytochromes (named Omc- E, S, and Z, respectively) from Geobacter sulfurreducens are investigated with the Pathways model for electron tunneling, classical molecular dynamics, and hybrid quantum/classical molecular mechanics. Thermally averaged electronic couplings for through-space heme-to-heme electron transfer in the "nanowires" computed with density functional theory are ≤0.015 eV. Pathways analyses also indicate that couplings match within a factor of 5 for all "nanowires", but some alternative tunneling routes are found involving covalent protein backbone bonds (Omc- S and Z) or propionic acid-ligating His H-bonds on adjacent hemes (OmcZ). Reorganization energies computed from electrostatic vertical energy gaps or a version of the Marcus continuum expression parameterized on the total (donor + acceptor) solvent-accessible surface area typically agree within 20% and fall within the range 0.48-0.98 eV. Reaction free energies in all three "nanowires" are ≤|0.28| eV, even though Coulombic interactions primarily tune the site redox energies by 0.7-1.2 eV. Given the conserved energetic parameters, redox conductivity differs by < 103-fold among the cytochrome "nanowires". Redox currents do not exceed 3.0 × 10-3 pA at a physiologically relevant 0.1 V bias, with the slowest electron transfers being on a (μs) timescale much faster than typical (ms) enzymatic turnovers. Thus, the "nanowires" are proposed to be functionally robust to variations in structure that provide a habitat-customized protein interface. The 30 pA to 30 nA variation in conductivity previously reported from atomic force microscopy experiments is not intrinsic to the structures and/or does not result from the physiologically relevant redox conduction mechanism.
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Affiliation(s)
- Matthew J Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, Connecticut 06510, United States
- Microbial Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut 06516, United States
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20
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Baquero DP, Cvirkaite-Krupovic V, Hu SS, Fields JL, Liu X, Rensing C, Egelman EH, Krupovic M, Wang F. Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes. Cell 2023; 186:2853-2864.e8. [PMID: 37290436 PMCID: PMC10330847 DOI: 10.1016/j.cell.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/04/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to numerous potential applications. However, whether other organisms employ similar ECNs for electron transfer remains unknown. Here, using cryoelectron microscopy, we describe the atomic structures of two ECNs from two major orders of hyperthermophilic archaea present in deep-sea hydrothermal vents and terrestrial hot springs. Homologs of Archaeoglobus veneficus ECN are widespread among mesophilic methane-oxidizing Methanoperedenaceae, alkane-degrading Syntrophoarchaeales archaea, and in the recently described megaplasmids called Borgs. The ECN protein subunits lack similarities in their folds; however, they share a common heme arrangement, suggesting an evolutionarily optimized heme packing for efficient electron transfer. The detection of ECNs in archaea suggests that filaments containing closely stacked hemes may be a common and widespread mechanism for long-range electron transfer in both prokaryotic domains of life.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France
| | | | - Shengen Shawn Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Jessie Lynda Fields
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France.
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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21
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Klein EM, Knoll MT, Gescher J. Microbe-Anode Interactions: Comparing the impact of genetic and material engineering approaches to improve the performance of microbial electrochemical systems (MES). Microb Biotechnol 2023; 16:1179-1202. [PMID: 36808480 PMCID: PMC10221544 DOI: 10.1111/1751-7915.14236] [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: 08/09/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/20/2023] Open
Abstract
Microbial electrochemical systems (MESs) are a highly versatile platform technology with a particular focus on power or energy production. Often, they are used in combination with substrate conversion (e.g., wastewater treatment) and production of value-added compounds via electrode-assisted fermentation. This rapidly evolving field has seen great improvements both technically and biologically, but this interdisciplinarity sometimes hampers overseeing strategies to increase process efficiency. In this review, we first briefly summarize the terminology of the technology and outline the biological background that is essential for understanding and thus improving MES technology. Thereafter, recent research on improvements at the biofilm-electrode interface will be summarized and discussed, distinguishing between biotic and abiotic approaches. The two approaches are then compared, and resulting future directions are discussed. This mini-review therefore provides basic knowledge of MES technology and the underlying microbiology in general and reviews recent improvements at the bacteria-electrode interface.
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Affiliation(s)
- Edina M. Klein
- Institute of Technical MicrobiologyUniversity of Technology HamburgHamburgGermany
| | - Melanie T. Knoll
- Institute of Technical MicrobiologyUniversity of Technology HamburgHamburgGermany
| | - Johannes Gescher
- Institute of Technical MicrobiologyUniversity of Technology HamburgHamburgGermany
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22
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Myers B, Catrambone F, Allen S, Hill PJ, Kovacs K, Rawson FJ. Engineering nanowires in bacteria to elucidate electron transport structural-functional relationships. Sci Rep 2023; 13:8843. [PMID: 37258594 DOI: 10.1038/s41598-023-35553-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells' bioenergetic programming. Their role is thought to be linked to facilitating electron transfer between cells and the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineered Cupriavidus necator H16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using a Cupriavidus necator chassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.
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Affiliation(s)
- Ben Myers
- Bioelectronics Laboratory, Regenerative Medicine and Cellular Therapies, School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Molecular Therapeutics and Formulation Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Francesco Catrambone
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Stephanie Allen
- Molecular Therapeutics and Formulation Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Phil J Hill
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
| | - Katalin Kovacs
- Bioelectronics Laboratory, Regenerative Medicine and Cellular Therapies, School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
- Molecular Therapeutics and Formulation Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Frankie J Rawson
- Bioelectronics Laboratory, Regenerative Medicine and Cellular Therapies, School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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23
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Yan Y, Zhang J, Tian L, Yan X, Du L, Leininger A, Zhang M, Li N, Ren ZJ, Wang X. DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate. WATER RESEARCH 2023; 235:119911. [PMID: 36989806 DOI: 10.1016/j.watres.2023.119911] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/27/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at -0.2 V where an abundance of Geobacter (49%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.
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Affiliation(s)
- Yuqing Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China; Deptartment of Civil and Environmental Engineering, Princeton University, 41 Olden St. Princeton, NJ 08540, USA; Andlinger Center for Energy and the Environment, Princeton University, 41 Olden St. Princeton, NJ 08540, USA
| | - Jiayao Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Lili Tian
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Lin Du
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Aaron Leininger
- Deptartment of Civil and Environmental Engineering, Princeton University, 41 Olden St. Princeton, NJ 08540, USA; Andlinger Center for Energy and the Environment, Princeton University, 41 Olden St. Princeton, NJ 08540, USA
| | - Mou Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 35 Yaguan Road, Jinnan District, Tianjin 300350, China
| | - Zhiyong Jason Ren
- Deptartment of Civil and Environmental Engineering, Princeton University, 41 Olden St. Princeton, NJ 08540, USA; Andlinger Center for Energy and the Environment, Princeton University, 41 Olden St. Princeton, NJ 08540, USA.
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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24
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Zhang B, Shi S, Tang R, Qiao C, Yang M, You Z, Shao S, Wu D, Yu H, Zhang J, Cao Y, Li F, Song H. Recent advances in enrichment, isolation, and bio-electrochemical activity evaluation of exoelectrogenic microorganisms. Biotechnol Adv 2023; 66:108175. [PMID: 37187358 DOI: 10.1016/j.biotechadv.2023.108175] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Exoelectrogenic microorganisms (EEMs) catalyzed the conversion of chemical energy to electrical energy via extracellular electron transfer (EET) mechanisms, which underlay diverse bio-electrochemical systems (BES) applications in clean energy development, environment and health monitoring, wearable/implantable devices powering, and sustainable chemicals production, thereby attracting increasing attentions from academic and industrial communities in the recent decades. However, knowledge of EEMs is still in its infancy as only ~100 EEMs of bacteria, archaea, and eukaryotes have been identified, motivating the screening and capture of new EEMs. This review presents a systematic summarization on EEM screening technologies in terms of enrichment, isolation, and bio-electrochemical activity evaluation. We first generalize the distribution characteristics of known EEMs, which provide a basis for EEM screening. Then, we summarize EET mechanisms and the principles underlying various technological approaches to the enrichment, isolation, and bio-electrochemical activity of EEMs, in which a comprehensive analysis of the applicability, accuracy, and efficiency of each technology is reviewed. Finally, we provide a future perspective on EEM screening and bio-electrochemical activity evaluation by focusing on (i) novel EET mechanisms for developing the next-generation EEM screening technologies, and (ii) integration of meta-omics approaches and bioinformatics analyses to explore nonculturable EEMs. This review promotes the development of advanced technologies to capture new EEMs.
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Affiliation(s)
- Baocai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Sicheng Shi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Tang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chunxiao Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Meiyi Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shulin Shao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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25
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Song B, Wang Z, Wang L, Wang Q, Li J, Song M, Ali J, Wang Y, Glebov EM, Zhuang X. In Situ Enhanced Yields of Microbial Nanowires: The Key Role of Environmental Stress. ACS Biomater Sci Eng 2023. [PMID: 37146257 DOI: 10.1021/acsbiomaterials.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The conductive microbial nanowires of Geobacter sulfurreducens serve as a model for long-range extracellular electron transfer (EET), which is considered a revolutionary "green" nanomaterial in the fields of bioelectronics, renewable energy, and bioremediation. However, there is no efficient pathway to induce microorganisms to express a large amount of microbial nanowires. Here, several strategies have been used to successfully induce the expression of microbial nanowires. Microbial nanowire expression was closely related to the concentration of electron acceptors. The microbial nanowire was around 17.02 μm in length, more than 3 times compared to its own length. The graphite electrode was used as an alternative electron acceptor by G. sulfurreducens, which obtained a fast start-up time of 44 h in microbial fuel cells (MFCs). Meanwhile, Fe(III) citrate-coated sugarcane carbon and biochar were prepared to test the applicability of these strategies in the actual microbial community. The unsatisfied EET efficiency between c-type cytochrome and extracellular insoluble electron receptors promoted the expression of microbial nanowires. Hence, microbial nanowires were proposed to be an effective survival strategy for G. sulfurreducens to cope with various environmental stresses. Based on this top-down strategy of artificially constructed microbial environmental stress, this study is of great significance for exploring more efficient methods to induce microbial nanowires expression.
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Affiliation(s)
- Bo Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhibin Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qi Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450003, China
| | - Jiaxin Li
- Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang 110819, China
| | - Manjiao Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jafar Ali
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China
| | - Yaxin Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Evgeni M Glebov
- Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, 3 Institutskaya Str., Novosibirsk 630090, Russian Federation
- Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russian Federation
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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26
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You Z, Li J, Wang Y, Wu D, Li F, Song H. Advances in mechanisms and engineering of electroactive biofilms. Biotechnol Adv 2023; 66:108170. [PMID: 37148984 DOI: 10.1016/j.biotechadv.2023.108170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/22/2023] [Accepted: 05/02/2023] [Indexed: 05/08/2023]
Abstract
Electroactive biofilms (EABs) are electroactive microorganisms (EAMs) encased in conductive polymers that are secreted by EAMs and formed by the accumulation and cross-linking of extracellular polysaccharides, proteins, nucleic acids, lipids, and other components. EABs are present in the form of multicellular aggregates and play a crucial role in bioelectrochemical systems (BESs) for diverse applications, including biosensors, microbial fuel cells for renewable bioelectricity production and remediation of wastewaters, and microbial electrosynthesis of valuable chemicals. However, naturally occurred EABs are severely limited owing to their low electrical conductivity that seriously restrict the electron transfer efficiency and practical applications. In the recent decade, synthetic biology strategies have been adopted to elucidate the regulatory mechanisms of EABs, and to enhance the formation and electrical conductivity of EABs. Based on the formation of EABs and extracellular electron transfer (EET) mechanisms, the synthetic biology-based engineering strategies of EABs are summarized and reviewed as follows: (i) Engineering the structural components of EABs, including strengthening the synthesis and secretion of structural elements such as polysaccharides, eDNA, and structural proteins, to improve the formation of biofilms; (ii) Enhancing the electron transfer efficiency of EAMs, including optimizing the distribution of c-type cytochromes and conducting nanowire assembly to promote contact-based EET, and enhancing electron shuttles' biosynthesis and secretion to promote shuttle-mediated EET; (iii) Incorporating intracellular signaling molecules in EAMs, including quorum sensing systems, secondary messenger systems, and global regulatory systems, to increase the electron transfer flux in EABs. This review lays a foundation for the design and construction of EABs for diverse BES applications.
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Affiliation(s)
- Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianxun Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yuxuan Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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27
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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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28
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Fessler M, Madsen JS, Zhang Y. Conjugative plasmids inhibit extracellular electron transfer in Geobacter sulfurreducens. Front Microbiol 2023; 14:1150091. [PMID: 37007462 PMCID: PMC10063792 DOI: 10.3389/fmicb.2023.1150091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
Geobacter sulfurreducens is part of a specialized group of microbes with the unique ability to exchange electrons with insoluble materials, such as iron oxides and electrodes. Therefore, G. sulfurreducens plays an essential role in the biogeochemical iron cycle and microbial electrochemical systems. In G. sulfurreducens this ability is primarily dependent on electrically conductive nanowires that link internal electron flow from metabolism to solid electron acceptors in the extracellular environment. Here we show that when carrying conjugative plasmids, which are self-transmissible plasmids that are ubiquitous in environmental bacteria, G. sulfurreducens reduces insoluble iron oxides at much slower rates. This was the case for all three conjugative plasmids tested (pKJK5, RP4 and pB10). Growth with electron acceptors that do not require expression of nanowires was, on the other hand, unaffected. Furthermore, iron oxide reduction was also inhibited in Geobacter chapellei, but not in Shewanella oneidensis where electron export is nanowire-independent. As determined by transcriptomics, presence of pKJK5 reduces transcription of several genes that have been shown to be implicated in extracellular electron transfer in G. sulfurreducens, including pilA and omcE. These results suggest that conjugative plasmids can in fact be very disadvantageous for the bacterial host by imposing specific phenotypic changes, and that these plasmids may contribute to shaping the microbial composition in electrode-respiring biofilms in microbial electrochemical reactors.
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Affiliation(s)
- Mathias Fessler
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Yifeng Zhang,
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29
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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30
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Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
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Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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31
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Guberman-Pfeffer MJ. Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire. J Phys Chem B 2022; 126:10083-10097. [PMID: 36417757 PMCID: PMC9743091 DOI: 10.1021/acs.jpcb.2c06822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨Hmn⟩), reaction free energies (ΔGmn), reorganization energies (λmn), and activation energies (Ea) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔGmn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.
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Affiliation(s)
- Matthew J. Guberman-Pfeffer
- Department
of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, Connecticut06510, United States,Microbial
Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut06516, United States,
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Towards engineering application: Integrating current strategies of promoting direct interspecies electron transfer to enhance anaerobic digestion. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Edel M, Philipp LA, Lapp J, Reiner J, Gescher J. Electron transfer of extremophiles in bioelectrochemical systems. Extremophiles 2022; 26:31. [PMID: 36222927 PMCID: PMC9556394 DOI: 10.1007/s00792-022-01279-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022]
Abstract
The interaction of bacteria and archaea with electrodes is a relatively new research field which spans from fundamental to applied research and influences interdisciplinary research in the fields of microbiology, biochemistry, biotechnology as well as process engineering. Although a substantial understanding of electron transfer processes between microbes and anodes and between microbes and cathodes has been achieved in mesophilic organisms, the mechanisms used by microbes under extremophilic conditions are still in the early stages of discovery. Here, we review our current knowledge on the biochemical solutions that evolved for the interaction of extremophilic organisms with electrodes. To this end, the available knowledge on pure cultures of extremophilic microorganisms has been compiled and the study has been extended with the help of bioinformatic analyses on the potential distribution of different electron transfer mechanisms in extremophilic microorganisms.
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Affiliation(s)
- Miriam Edel
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Laura-Alina Philipp
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Jonas Lapp
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Johannes Reiner
- Karlsruhe Institute of Technology, Engler-Bunte-Institute, Karlsruhe, Germany
| | - Johannes Gescher
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany.
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Myers B, Hill P, Rawson F, Kovács K. Enhancing Microbial Electron Transfer Through Synthetic Biology and Biohybrid Approaches: Part II : Combining approaches for clean energy. JOHNSON MATTHEY TECHNOLOGY REVIEW 2022. [DOI: 10.1595/205651322x16621070592195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
It is imperative to develop novel processes that rely on cheap, sustainable and abundant resources whilst providing carbon circularity. Microbial electrochemical technologies (MET) offer unique opportunities to facilitate the conversion of chemicals to electrical energy or vice versa
by harnessing the metabolic processes of bacteria to valorise a range of waste products including greenhouse gases (GHGs). Part I (1) introduced the EET pathways, their limitations and applications. Here in Part II, we outline the strategies researchers have used to modulate microbial electron
transfer, through synthetic biology and biohybrid approaches and present the conclusions and future directions.
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Affiliation(s)
- Benjamin Myers
- Bioelectronics Laboratory, Regenerative Medicine and Cellular Therapies Division, School of Pharmacy, Biodiscovery Institute, University of Nottingham University Park, Clifton Boulevard, Nottingham, NG7 2RD UK
| | - Phil Hill
- School of Biosciences, University of Nottingham Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Frankie Rawson
- Bioelectronics Laboratory, Regenerative Medicine and Cellular Therapies Division, School of Pharmacy, Biodiscovery Institute, University of Nottingham University Park, Clifton Boulevard, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- School of Pharmacy, Boots Science Building, University of Nottingham, University Park Clifton Boulevard, Nottingham, NG7 2RD UK
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35
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Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Nat Microbiol 2022; 7:1291-1300. [PMID: 35798889 PMCID: PMC9357133 DOI: 10.1038/s41564-022-01159-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
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36
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37
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Pereira J, de Nooy S, Sleutels T, Ter Heijne A. Opportunities for visual techniques to determine characteristics and limitations of electro-active biofilms. Biotechnol Adv 2022; 60:108011. [PMID: 35753624 DOI: 10.1016/j.biotechadv.2022.108011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/10/2022] [Accepted: 06/18/2022] [Indexed: 11/02/2022]
Abstract
Optimization of bio-electrochemical systems (BESs) relies on a better understanding of electro-active biofilms (EABfs). These microbial communities are studied with a range of techniques, including electrochemical, visual and chemical techniques. Even though each of these techniques provides very valuable and wide-ranging information about EABfs, such as performance, morphology and biofilm composition, they are often destructive. Therefore, the information obtained from EABfs development and characterization studies are limited to a single characterization of EABfs and often limited to one time point that determines the end of the experiment. Despite being scarcer and not as commonly reported as destructive techniques, non-destructive visual techniques can be used to supplement EABfs characterization by adding in-situ information of EABfs functioning and its development throughout time. This opens the door to EABfs monitoring studies that can complement the information obtained with destructive techniques. In this review, we provide an overview of visual techniques and discuss the opportunities for combination with the established electrochemical techniques to study EABfs. By providing an overview of suitable visual techniques and discussing practical examples of combination of visual with electrochemical methods, this review aims at serving as a source of inspiration for future studies in the field of BESs.
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Affiliation(s)
- João Pereira
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands; Environmental Technology, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - Sam de Nooy
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands; Environmental Technology, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - Tom Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands; Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands.
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Dahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O’Brien JP, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. SCIENCE ADVANCES 2022; 8:eabm7193. [PMID: 35544567 PMCID: PMC9094664 DOI: 10.1126/sciadv.abm7193] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/28/2022] [Indexed: 06/10/2023]
Abstract
Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>1010 s-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.
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Affiliation(s)
- Peter J. Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sophia M. Yi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Yangqi Gu
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Catharine Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jens Neu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - J. Patrick O’Brien
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Matthew J. Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Dennis Vu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | | | - Nikhil S. Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
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Deng X, Luo D, Okamoto A. Defined and unknown roles of conductive nanoparticles for the enhancement of microbial current generation: A review. BIORESOURCE TECHNOLOGY 2022; 350:126844. [PMID: 35158034 DOI: 10.1016/j.biortech.2022.126844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The ability of various bacteria to make use of solid substrates through extracellular electron transfer (EET) or extracellular electron uptake (EEU) has enabled the development of valuable biotechnologies such as microbial fuel cells (MFCs) and microbial electrosynthesis (MES). It is common practice to use metallic and semiconductive nanoparticles (NPs) for microbial current enhancement. However, the effect of NPs is highly variable between systems, and there is no clear guideline for effectively increasing the current generation. In the present review, the proposed mechanisms for enhancing current production in MFCs and MES are summarized, and the critical factors for NPs to enhance microbial current generation are discussed. Implications for microbially induced iron corrosion, where iron sulfide NPs are proposed to enhance the rate of EEU, photochemically driven MES, and several future research directions to further enhance microbial current generation, are also discussed.
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Affiliation(s)
- Xiao Deng
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Dan Luo
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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40
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From iron to bacterial electroconductive filaments: Exploring cytochrome diversity using Geobacter bacteria. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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41
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Garnett JA, Atherton J. Structure Determination of Microtubules and Pili: Past, Present, and Future Directions. Front Mol Biosci 2022; 8:830304. [PMID: 35096976 PMCID: PMC8795688 DOI: 10.3389/fmolb.2021.830304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 11/30/2022] Open
Abstract
Historically proteins that form highly polymeric and filamentous assemblies have been notoriously difficult to study using high resolution structural techniques. This has been due to several factors that include structural heterogeneity, their large molecular mass, and available yields. However, over the past decade we are now seeing a major shift towards atomic resolution insight and the study of more complex heterogenous samples and in situ/ex vivo examination of multi-subunit complexes. Although supported by developments in solid state nuclear magnetic resonance spectroscopy (ssNMR) and computational approaches, this has primarily been due to advances in cryogenic electron microscopy (cryo-EM). The study of eukaryotic microtubules and bacterial pili are good examples, and in this review, we will give an overview of the technical innovations that have enabled this transition and highlight the advancements that have been made for these two systems. Looking to the future we will also describe systems that remain difficult to study and where further technical breakthroughs are required.
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Affiliation(s)
- James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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42
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Clarke TA. Plugging into bacterial nanowires: a comparison of model electrogenic organisms. Curr Opin Microbiol 2022; 66:56-62. [PMID: 34999354 DOI: 10.1016/j.mib.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022]
Abstract
Extracellular electron transport (EET) is an important metabolic process used by many bacteria to remove excess electrons generated through cellular metabolism. However, there is still limited understanding about how the molecular mechanisms used to export electrons impact cellular metabolism. Here the EET pathways of two of the best-studied electrogenic organisms, Shewanella oneidensis and Geobacter sulferreducens, are described. Both organisms have superficially similar overall EET routes, but differ in the mechanisms used to oxidise menaquinol, transfer electrons across the outer membrane and reduce extracellular substrates. These mechanistic differences substantially impact both substrate choice and bacterial lifestyle.
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Affiliation(s)
- Thomas Andrew Clarke
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom.
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43
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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Making protons tag along with electrons. Biochem J 2021; 478:4093-4097. [PMID: 34871365 DOI: 10.1042/bcj20210592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
Abstract
Every living cell needs to get rid of leftover electrons when metabolism extracts energy through the oxidation of nutrients. Common soil microbes such as Geobacter sulfurreducens live in harsh environments that do not afford the luxury of soluble, ingestible electron acceptors like oxygen. Instead of resorting to fermentation, which requires the export of reduced compounds (e.g. ethanol or lactate derived from pyruvate) from the cell, these organisms have evolved a means to anaerobically respire by using nanowires to export electrons to extracellular acceptors in a process called extracellular electron transfer (EET) [ 1]. Since 2005, these nanowires were thought to be pili filaments [ 2]. But recent studies have revealed that nanowires are composed of multiheme cytochromes OmcS [ 3, 4] and OmcZ [ 5] whereas pili remain inside the cell during EET and are required for the secretion of nanowires [ 6]. However, how electrons are passed to these nanowires remains a mystery ( Figure 1A). Periplasmic cytochromes (Ppc) called PpcA-E could be doing the job, but only two of them (PpcA and PpcD) can couple electron/proton transfer - a necessary condition for energy generation. In a recent study, Salgueiro and co-workers selectively replaced an aromatic with an aliphatic residue to couple electron/proton transfer in PpcB and PpcE (Biochem. J. 2021, 478 (14): 2871-2887). This significant in vitro success of their protein engineering strategy may enable the optimization of bioenergetic machinery for bioenergy, biofuels, and bioelectronics applications.
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Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
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Draft Genome Sequences of the Ferric Iron-Reducing Geobacter sp. Strains AOG1 and AOG2, Isolated from Enrichment Cultures on Crystalline Iron(III) Oxides. Microbiol Resour Announc 2021; 10:e0091321. [PMID: 34734763 PMCID: PMC8567784 DOI: 10.1128/mra.00913-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequences of two Geobacter sp. strains, AOG1 and AOG2, isolated from enrichment cultures using crystalline Fe(III) oxides as electron acceptors. Strains AOG1 and AOG2 possess numerous genes encoding multiheme c-type cytochromes and pilA-N genes encoding the pilin monomer of nanowires in their genomes.
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McCuskey SR, Chatsirisupachai J, Zeglio E, Parlak O, Panoy P, Herland A, Bazan GC, Nguyen TQ. Current Progress of Interfacing Organic Semiconducting Materials with Bacteria. Chem Rev 2021; 122:4791-4825. [PMID: 34714064 DOI: 10.1021/acs.chemrev.1c00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial bioelectronics require interfacing microorganisms with electrodes. The resulting abiotic/biotic platforms provide the basis of a range of technologies, including energy conversion and diagnostic assays. Organic semiconductors (OSCs) provide a unique strategy to modulate the interfaces between microbial systems and external electrodes, thereby improving the performance of these incipient technologies. In this review, we explore recent progress in the field on how OSCs, and related materials capable of charge transport, are being used within the context of microbial systems, and more specifically bacteria. We begin by examining the electrochemical communication modes in bacteria and the biological basis for charge transport. Different types of synthetic organic materials that have been designed and synthesized for interfacing and interrogating bacteria are discussed next, followed by the most commonly used characterization techniques for evaluating transport in microbial, synthetic, and hybrid systems. A range of applications is subsequently examined, including biological sensors and energy conversion systems. The review concludes by summarizing what has been accomplished so far and suggests future design approaches for OSC bioelectronics materials and technologies that hybridize characteristic properties of microbial and OSC systems.
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Affiliation(s)
- Samantha R McCuskey
- Department of Chemistry, National University of Singapore, Singapore 119077, Singapore
| | - Jirat Chatsirisupachai
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand
| | - Erica Zeglio
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 17177, Sweden
| | - Onur Parlak
- Dermatology and Venereology Division, Department of Medicine(Solna), Karolinska Institute, Stockholm 17177, Sweden.,AIMES Center of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Patchareepond Panoy
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand
| | - Anna Herland
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 17177, Sweden.,AIMES Center of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Guillermo C Bazan
- Department of Chemistry, National University of Singapore, Singapore 119077, Singapore
| | - Thuc-Quyen Nguyen
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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Cytochrome OmcS is not essential for extracellular electron transport via conductive pili in Geobacter sulfurreducens strain KN400. Appl Environ Microbiol 2021; 88:e0162221. [PMID: 34669448 DOI: 10.1128/aem.01622-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The multi-heme c-type cytochrome OmcS is one of the central components for extracellular electron transport in Geobacter sulfurreducens strain DL-1, but its role in other microbes, including other strains of G. sulfurreducens is currently a matter of debate. Therefore, we investigated the function of OmcS in G. sulfurreducens strain KN400, which is even more effective in extracellular electron transfer than strain DL-1. We found that deleting omcS from strain KN400 did not negatively impact the rate of Fe(III) oxide reduction and that the cells expressed conductive filaments. Replacing the wild-type pilin gene with the aro-5 pilin gene eliminated the OmcS-deficient strain's ability for electron transport to insoluble electron acceptors and diminished filament conductivity. These results are consistent with the concept that electrically conductive pili are the primary conduit for long-range electron transfer in G. sulfurreducens and closely related species. These findings, coupled with the lack of OmcS homologs in most other microbes capable of extracellular electron transfer, suggest that OmcS is not a common critical component for extracellular electron transfer. Importance OmcS has been widely studied and noted to be one of the key components for extracellular electron exchange by Geobacter sulfurreducens strain DL-1. However, the true importance of OmcS warrants further investigation as it is well-known that very few bacteria, even within the Geobacteraceae family, contain OmcS homologs, and many bacteria capable of extracellular electron transfer lack an abundance of any type of outer-surface c-type cytochrome. In addition, there is much debate regarding the importance of OmcS filaments in the mechanism of extracellular electron transport to insoluble electron acceptors by G. sulfurreducens. It has been suggested that filaments comprised of OmcS, rather than e-pili, are the predominant conductive filaments expressed by G. sulfurreducens. However, the results presented in this manuscript, along with multiple other lines of evidence, indicate that OmcS filaments cannot be the primary conductive protein nanowires expressed by G. sulfurreducens.
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Dong F, Lee YS, Gaffney EM, Liou W, Minteer SD. Engineering Cyanobacterium with Transmembrane Electron Transfer Ability for Bioelectrochemical Nitrogen Fixation. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fangyuan Dong
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Yoo Seok Lee
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Erin M. Gaffney
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Willisa Liou
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
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Nanosecond heme-to-heme electron transfer rates in a multiheme cytochrome nanowire reported by a spectrally unique His/Met-ligated heme. Proc Natl Acad Sci U S A 2021; 118:2107939118. [PMID: 34556577 PMCID: PMC8488605 DOI: 10.1073/pnas.2107939118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/29/2022] Open
Abstract
Multiheme cytochromes have been identified as essential proteins for electron exchange between bacterial enzymes and redox substrates outside of the cell. In microbiology, these proteins contribute to efficient energy storage and conversion. For biotechnology, multiheme cytochromes contribute to the production of green fuels and electricity. Furthermore, these proteins inspire the design of molecular-scale electronic devices. Here, we report exceptionally high rates of heme-to-heme electron transfer in a multiheme cytochrome. We expect similarly high rates, among the highest reported for ground-state electron transfer in biology, in other multiheme cytochromes as the close-packed hemes adopt similar configurations despite very different amino acid sequences and protein folds. Proteins achieve efficient energy storage and conversion through electron transfer along a series of redox cofactors. Multiheme cytochromes are notable examples. These proteins transfer electrons over distance scales of several nanometers to >10 μm and in so doing they couple cellular metabolism with extracellular redox partners including electrodes. Here, we report pump-probe spectroscopy that provides a direct measure of the intrinsic rates of heme–heme electron transfer in this fascinating class of proteins. Our study took advantage of a spectrally unique His/Met-ligated heme introduced at a defined site within the decaheme extracellular MtrC protein of Shewanella oneidensis. We observed rates of heme-to-heme electron transfer on the order of 109 s−1 (3.7 to 4.3 Å edge-to-edge distance), in good agreement with predictions based on density functional and molecular dynamics calculations. These rates are among the highest reported for ground-state electron transfer in biology. Yet, some fall 2 to 3 orders of magnitude below the Moser–Dutton ruler because electron transfer at these short distances is through space and therefore associated with a higher tunneling barrier than the through-protein tunneling scenario that is usual at longer distances. Moreover, we show that the His/Met-ligated heme creates an electron sink that stabilizes the charge separated state on the 100-μs time scale. This feature could be exploited in future designs of multiheme cytochromes as components of versatile photosynthetic biohybrid assemblies.
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