1
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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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2
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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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3
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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: 9] [Impact Index Per Article: 4.5] [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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4
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Mao S, Sun B, Zhou G, Guo T, Wang J, Zhao Y. Applications of biomemristors in next generation wearable electronics. NANOSCALE HORIZONS 2022; 7:822-848. [PMID: 35697026 DOI: 10.1039/d2nh00163b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With the rapid development of mobile internet and artificial intelligence, wearable electronic devices have a great market prospect. In particular, information storage and processing of real-time collected data are an indispensable part of wearable electronic devices. Biomaterial-based memristive systems are suitable for storage and processing of the obtained information in wearable electronics due to the accompanying merits, i.e. sustainability, lightweight, degradability, low power consumption, flexibility and biocompatibility. So far, many biomaterial-based flexible and wearable memristive devices were prepared by spin coating or other technologies on a flexible substrate at room temperature. However, mechanical deformation caused by mechanical mismatch between devices and soft tissues leads to the instability of device performance. From the current research and practical application, the device will face great challenges when adapting to different working environments. In fact, some interesting studies have been performed to address the above issues while they were not intensively highlighted and overviewed. Herein, the progress in wearable biomemristive devices is reviewed, and the outlook and perspectives are provided in consideration of the existing challenges during the development of wearable biomemristive systems.
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Affiliation(s)
- Shuangsuo Mao
- Fujian Provincial Collaborative Innovation Center for Advanced High-Field Superconducting Materials and Engineering, Fujian Normal University, Fuzhou, Fujian 350117, China.
- College of Physics and Energy, Fujian Normal University, Fuzhou, Fujian 351007, China
| | - Bai Sun
- Fujian Provincial Collaborative Innovation Center for Advanced High-Field Superconducting Materials and Engineering, Fujian Normal University, Fuzhou, Fujian 350117, China.
- College of Physics and Energy, Fujian Normal University, Fuzhou, Fujian 351007, China
- School of Physical Science and Technology, Key Laboratory of Advanced Technology of Materials, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
- Superconductivity and New Energy R&D Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Guangdong Zhou
- Scholl of Artificial Intelligence, Southwest University, Chongqing, 400715, China
| | - Tao Guo
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Centre for Advanced Materials Joining, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jiangqiu Wang
- School of Physical Science and Technology, Key Laboratory of Advanced Technology of Materials, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
- Superconductivity and New Energy R&D Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Yong Zhao
- Fujian Provincial Collaborative Innovation Center for Advanced High-Field Superconducting Materials and Engineering, Fujian Normal University, Fuzhou, Fujian 350117, China.
- College of Physics and Energy, Fujian Normal University, Fuzhou, Fujian 351007, China
- School of Physical Science and Technology, Key Laboratory of Advanced Technology of Materials, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
- Superconductivity and New Energy R&D Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
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5
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Kong Z, Zhou Y, Fu Z, Zhang Y, Yan R. Mechanism of stable power generation and nitrogen removal in the ANAMMOX-MFC treating low C/N wastewater. CHEMOSPHERE 2022; 296:133937. [PMID: 35167835 DOI: 10.1016/j.chemosphere.2022.133937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/14/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the mechanism of enhanced power generation and nitrogen removal in an ANAMMOX-MFC reactor through subsequent acetate addition. Data showed that nearly 99% total nitrogen removal (≤1 mg L-1) and 1.41 W m-3 power generation were achieved synchronously under low COD/N (∼1.5) after the subsequent addition of acetate (100 mgCOD·L-1). The columbic efficiency of the system has increased by 15 times (from 0.64% to 9.48%) after adding acetate. Batch tests showed that the denitrification and ANAMMOX progress occurred synchronously before acetate addition the nitrogen removal rate was accelerated. A distinct shift of bacterial community driven by acetate addition was discovered. The high throughput sequencing analysis indicated acetate addition stimulated the enrichment of denitrifiers, such as Aquimonas, Bradyrhizobium, Thauera, and the potential exoelectrogens changing from Comamonas to Pseudomonas. Functional genes forecasts based on KEGG database and COG database showed that the expressions of TCA functional genes were highly promoted in ANAMMOX-MFC, which demonstrated the enhanced electron transfer pathway driven by acetate addition under low COD/N ratio.
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Affiliation(s)
- Zhiyuan Kong
- Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010031, China; Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Yongheng Zhou
- Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010031, China
| | - Zhimin Fu
- Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010031, China.
| | - Yuancan Zhang
- Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010031, China
| | - Rong Yan
- Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010031, China
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6
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He X, Chadwick G, Jiménez Otero F, Orphan V, Meile C. Spatially Resolved Electron Transport through Anode‐Respiring
Geobacter sulfurreducens
Biofilms: Controls and Constraints. ChemElectroChem 2021. [DOI: 10.1002/celc.202100111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaojia He
- Department of Marine Sciences University of Georgia Athens GA USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | | | - Victoria Orphan
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | - Christof Meile
- Department of Marine Sciences University of Georgia Athens GA USA
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7
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Halaby S, Martynowycz M, Zhu Z, Tretiak S, Zhugayevych A, Gonen T, Seifrid M. Microcrystal Electron Diffraction for Molecular Design of Functional Non-Fullerene Acceptor Structures. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:966-977. [PMID: 36942096 PMCID: PMC10024952 DOI: 10.1021/acs.chemmater.0c04111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding the relationship between molecular structure and solid-state arrangement informs about the design of new organic semiconductor (OSC) materials with improved optoelectronic properties. However, determining their atomic structure remains challenging. Here, we report the lattice organization of two non-fullerene acceptors (NFAs) determined using microcrystal electron diffraction (MicroED) from crystals not traceable by X-ray crystallography. The MicroED structure of o-IDTBR was determined from a powder without crystallization, and a new polymorph of ITIC-Th is identified with the most distorted backbone of any NFA. Electronic structure calculations elucidate the relationships between molecular structures, lattice arrangements, and charge-transport properties for a number of NFA lattices. The high dimensionality of the connectivity of the 3D wire mesh topology is the best for robust charge transport within NFA crystals. However, some examples suffer from uneven electronic coupling. MicroED combined with advanced electronic structure modeling is a powerful new approach for structure determination, exploring polymorphism and guiding the design of new OSCs and NFAs.
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Affiliation(s)
- Steve Halaby
- Howard Hughes Medical Institute, David Geffen School of Medicine, Department of Biological Chemistry and Physiology, University of California, Los Angeles, California 90095, United States
| | - Michael Martynowycz
- Howard Hughes Medical Institute, David Geffen School of Medicine, Department of Biological Chemistry and Physiology, University of California, Los Angeles, California 90095, United States
| | - Ziyue Zhu
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States; Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | | | - Tamir Gonen
- Howard Hughes Medical Institute, David Geffen School of Medicine, Department of Biological Chemistry and Physiology, University of California, Los Angeles, California 90095, United States
| | - Martin Seifrid
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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8
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Yalcin SE, Malvankar NS. The blind men and the filament: Understanding structures and functions of microbial nanowires. Curr Opin Chem Biol 2020; 59:193-201. [PMID: 33070100 PMCID: PMC7736336 DOI: 10.1016/j.cbpa.2020.08.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/20/2020] [Indexed: 12/18/2022]
Abstract
Extracellular electron transfer via filamentous protein appendages called 'microbial nanowires' has long been studied in Geobacter and other bacteria because of their crucial role in globally-important environmental processes and their applications for bioenergy, biofuels, and bioelectronics. Thousands of papers thought these nanowires as pili without direct evidence. Here, we summarize recent discoveries that could help resolve two decades of confounding observations. Using cryo-electron microscopy with multimodal functional imaging and a suite of electrical, biochemical, and physiological studies, we find that rather than pili, nanowires are composed of cytochromes OmcS and OmcZ that transport electrons via seamless stacking of hemes over micrometers. We discuss the physiological need for two different nanowires and their potential applications for sensing, synthesis, and energy production.
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Affiliation(s)
- Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA; Microbial Sciences Institute, Yale University, New Haven, CT, 06516, USA.
| | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA; Microbial Sciences Institute, Yale University, New Haven, CT, 06516, USA.
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9
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Roy S, Xie O, Dorval Courchesne N. Challenges in engineering conductive protein fibres: Disentangling the knowledge. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sophia Roy
- Department of Chemical Engineering McGill University Montréal Québec Canada
| | - Oliver Xie
- Department of Chemical Engineering McGill University Montréal Québec Canada
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10
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Eshel Y, Peskin U, Amdursky N. Coherence-assisted electron diffusion across the multi-heme protein-based bacterial nanowire. NANOTECHNOLOGY 2020; 31:314002. [PMID: 32259806 DOI: 10.1088/1361-6528/ab8767] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological electron transfer (ET) is one of the most studied biochemical processes due to its immense importance in biology. For many years, biological ET was explained using the classical incoherent transport mechanism, i.e. sequential hopping. One of the relatively recent major observations in this field is long-range extracellular ET (EET), where some bacteria were shown to mediate electrons for extremely long distances on the micrometer length scales across individual nanowires. This fascinating finding has resulted in several suggested mechanisms that might explain this intriguing EET. More recently, the structure of a conductive G. sulfurreducens nanowire has been solved, which showed a highly ordered quasi-1D wire of a hexaheme cytochrome protein, named OmcS. Based on this new structure, we suggest here several electron diffusion models for EET, involving either purely hopping or several degrees of mixed hopping and coherent transport, in which the coherent part is due to a local rigidification of the protein structure, associated with a decrease in the local reorganization energy. The effect is demonstrated for two closely packed heme sites as well as for longer chains containing up to several dozens porphyrins. We show that the pure hopping model probably cannot explain the reported conductivity values of the G. sulfurreducens nanowire using conventional values of reorganization energy and electronic coupling. On the other hand, we show that for a wide range of the latter energy values, the mixed hopping-coherent model results in superior electron diffusion compared to the pure hopping model, and especially for long-range coherent transport, involving multiple porphyrin sites.
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Affiliation(s)
- Yoni Eshel
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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11
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Shu C, Zhu Q, Xiao K, Hou Y, Ma H, Ma J, Sun X. Direct Extracellular Electron Transfer of the Geobacter sulfurreducens Pili Relevant to Interaromatic Distances. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6151587. [PMID: 31886232 PMCID: PMC6925702 DOI: 10.1155/2019/6151587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 01/05/2023]
Abstract
Microorganisms can transfer electrons directly to extracellular acceptors, during which organic compounds are oxidized to carbon dioxide. One of these microbes, Geobacter sulfurreducens, is well known for the "metallic-like" conductivity of its type IV pili. However, there is no consensus on what the mechanism for electron transfer along these conductive pili is. Based on the aromatic distances and orientations of our predicted models, the mechanism of electron transfer in the Geobacter sulfurreducens (GS) pili was explored by quantum chemical calculations with Marcus theory of electron transfer reactions. Three aromatic residues from the N-terminal α-helix of the GS pilin subunit are packed together, resulting in a continuous pi-pi interaction chain. The theoretical conductance (4.69 μS/3.85 μS) of the predicted models is very similar to that in the experiments reported recently (3.40 μS). These findings offer a new concept that the GS pili belongs to a new class of proteins that can transport electrons through pi-pi interaction between aromatic residues and also provide a valuable tool for guiding further researches of these conductive pili, to investigate their roles in biogeochemical cycling, and potential applications in biomaterials, bioelectronics, and bioenergy.
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Affiliation(s)
- Chuanjun Shu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Qiang Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering and Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing 210023, China
| | - Ke Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Haibo Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering and Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing 210023, China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering and Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing 210023, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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12
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Ru X, Zhang P, Beratan DN. Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili. J Phys Chem B 2019; 123:5035-5047. [PMID: 31095388 DOI: 10.1021/acs.jpcb.9b01086] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electrically conductive pili of Geobacter sulfurreducens are of both fundamental and practical interest. They facilitate extracellular and interspecies electron transfer (ET) and also provide an electrical interface between living and nonliving systems. We examine the possible mechanisms of G. sulfurreducens electron transfer in regimes ranging from incoherent to coherent transport. For plausible ET parameters, electron transfer in G. sulfurreducens bacterial nanowires mediated only by the protein is predicted to be dominated by incoherent hopping between phenylalanine (Phe) and tyrosine (Tyr) residues that are 3 to 4 Å apart, where Phe residues in the hopping pathways may create delocalized "islands." This mechanism could be accessible in the presence of strong oxidants that are capable of oxidizing Phe and Tyr residues. We also examine the physical requirements needed to sustain biological respiration via nanowires. We find that the hopping regimes with ET rates on the order of 108 s-1 between Phe islands and Tyr residues, and conductivities on the order of mS/cm, can support ET fluxes that are compatible with cellular respiration rates, although sustaining this delocalization in the heterogeneous protein environment may be challenging. Computed values of fully coherent electron fluxes through the pili are orders of magnitude too low to support microbial respiration. We suggest experimental probes of the transport mechanism based on mutant studies to examine the roles of aromatic amino acids and yet to be identified redox cofactors.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Peng Zhang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States.,Department of Physics , Duke University , Durham , North Carolina 27708 , United States
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13
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Danielsen SPO, Nguyen TQ, Fredrickson GH, Segalman RA. Complexation of a Conjugated Polyelectrolyte and Impact on Optoelectronic Properties. ACS Macro Lett 2019; 8:88-94. [PMID: 35619414 DOI: 10.1021/acsmacrolett.8b00924] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Electrostatic assembly of conjugated polyelectrolytes, which combine a π-conjugated polymer backbone with pendant ionic groups, offer an opportunity for tuning materials properties and a new route for formulating concentrated inks for printable electronics. Complex coacervation, a liquid-liquid phase separation upon complexation of oppositely charged polyelectrolytes in solution, is used to form dense suspensions of π-conjugated material. A model system of a cationic conjugated polyelectrolyte poly(3-[6'-{N-butylimidazolium}hexyl]thiophene) bromide and sodium poly(styrenesulfonate) dissolved in tetrahydrofuran-water mixtures was used to investigate this complexation behavior of conjugated polyelectrolytes in terms of electrostatic strength, solvent quality, and polymer concentration. The balance of electrostatic interaction between the oppositely charged polyelectrolytes together with their charge compensating counterions and solvent quality for the hydrophobic π-conjugated backbone leads to a rich phase diagram of soluble complexes, precipitates, and complex coacervates. The conjugated polyelectrolyte in the polyelectrolyte complexes has an increased π-conjugation length and enhanced emissivity, with ideal chain configurations due to the reduction of kink sites and torsional disorder. The advantageous photophysical properties in the dense liquid phases makes the scheme attractive for the large-scale processing of optoelectronic devices, chemical sensors, and bioelectronics components.
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14
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Gagkaeva ZV, Zhukova ES, Grinenko V, Grebenko AK, Sidoruk KV, Voeikova TA, Dressel M, Gorshunov BP. Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix. J Biol Phys 2018; 44:401-417. [PMID: 29732506 PMCID: PMC6082806 DOI: 10.1007/s10867-018-9497-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/13/2018] [Indexed: 01/30/2023] Open
Abstract
Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈ 200 and ≈ 600 cm-1, respectively. The sharp excitations seen above 1000 cm-1 are assigned to intramolecular vibrations.
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Affiliation(s)
- Z V Gagkaeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - E S Zhukova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - V Grinenko
- Institute for Metallic Materials, IFW Dresden, Dresden, Germany
| | - A K Grebenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - K V Sidoruk
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - T A Voeikova
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - M Dressel
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Physikalisches Institut, Universität Stuttgart, Stuttgart, Germany
| | - B P Gorshunov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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15
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Microbial electrocatalysis: Redox mediators responsible for extracellular electron transfer. Biotechnol Adv 2018; 36:1815-1827. [PMID: 30196813 DOI: 10.1016/j.biotechadv.2018.07.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 11/21/2022]
Abstract
Redox mediator plays an important role in extracellular electron transfer (EET) in many environments wherein microbial electrocatalysis occurs actively. Because of the block of cell envelope and the low difference of redox potential between the intracellular and extracellular surroundings, the proceeding of EET depends mainly on the help of a variety of mediators that function as an electron carrier or bridge. In this Review, we will summarize a wide range of redox mediators and further discuss their functional mechanisms in EET that drives a series of microbial electrocatalytic reactions. Studying these mediators adds to our knowledge of how charge transport and electrochemical reactions occur at the microorganism-electrode interface. This understanding would promote the widespread applications of microbial electrocatalysis in microbial fuel cells, bioremediation, bioelectrosynthesis, biomining, nanomaterial productions, etc. These improved applications will greatly benefit the sustainable development of the environmental-friendly biochemical industries.
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16
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Microbial nanowires - Electron transport and the role of synthetic analogues. Acta Biomater 2018; 69:1-30. [PMID: 29357319 DOI: 10.1016/j.actbio.2018.01.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 02/07/2023]
Abstract
Electron transfer is central to cellular life, from photosynthesis to respiration. In the case of anaerobic respiration, some microbes have extracellular appendages that can be utilised to transport electrons over great distances. Two model organisms heavily studied in this arena are Shewanella oneidensis and Geobacter sulfurreducens. There is some debate over how, in particular, the Geobacter sulfurreducens nanowires (formed from pilin nanofilaments) are capable of achieving the impressive feats of natural conductivity that they display. In this article, we outline the mechanisms of electron transfer through delocalised electron transport, quantum tunnelling, and hopping as they pertain to biomaterials. These are described along with existing examples of the different types of conductivity observed in natural systems such as DNA and proteins in order to provide context for understanding the complexities involved in studying the electron transport properties of these unique nanowires. We then introduce some synthetic analogues, made using peptides, which may assist in resolving this debate. Microbial nanowires and the synthetic analogues thereof are of particular interest, not just for biogeochemistry, but also for the exciting potential bioelectronic and clinical applications as covered in the final section of the review. STATEMENT OF SIGNIFICANCE Some microbes have extracellular appendages that transport electrons over vast distances in order to respire, such as the dissimilatory metal-reducing bacteria Geobacter sulfurreducens. There is significant debate over how G. sulfurreducens nanowires are capable of achieving the impressive feats of natural conductivity that they display: This mechanism is a fundamental scientific challenge, with important environmental and technological implications. Through outlining the techniques and outcomes of investigations into the mechanisms of such protein-based nanofibrils, we provide a platform for the general study of the electronic properties of biomaterials. The implications are broad-reaching, with fundamental investigations into electron transfer processes in natural and biomimetic materials underway. From these studies, applications in the medical, energy, and IT industries can be developed utilising bioelectronics.
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17
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Lebedev N, Griva I, Blom A, Tender LM. Effect of iron doping on protein molecular conductance. Phys Chem Chem Phys 2018; 20:14072-14081. [DOI: 10.1039/c8cp00656c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study analyzes the role of Fe in electron transfer through non-heme iron-containing proteins.
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Affiliation(s)
- Nikolai Lebedev
- Center for Bio-Molecular Science and Engineering
- U.S. Naval Research Laboratory
- Washington
- USA
| | - Igor Griva
- Department of Mathematical Sciences and Center for Simulation and Modeling
- George Mason University
- Fairfax
- USA
| | | | - Leonard M. Tender
- Center for Bio-Molecular Science and Engineering
- U.S. Naval Research Laboratory
- Washington
- USA
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18
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Panda SS, Katz HE, Tovar JD. Solid-state electrical applications of protein and peptide based nanomaterials. Chem Soc Rev 2018; 47:3640-3658. [DOI: 10.1039/c7cs00817a] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes recent advancements in electrical properties and applications of natural proteins and mutated variants, synthetic oligopeptides and peptide–π conjugates.
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Affiliation(s)
- Sayak Subhra Panda
- Department of Chemistry
- Krieger School of Arts and Sciences
- Johns Hopkins University
- Baltimore
- USA
| | - Howard E. Katz
- Department of Chemistry
- Krieger School of Arts and Sciences
- Johns Hopkins University
- Baltimore
- USA
| | - John D. Tovar
- Department of Chemistry
- Krieger School of Arts and Sciences
- Johns Hopkins University
- Baltimore
- USA
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19
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Structural Basis for the Influence of A1, 5A, and W51W57 Mutations on the Conductivity of the Geobacter sulfurreducens Pili. CRYSTALS 2017. [DOI: 10.3390/cryst8010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The metallic-like conductivity of the Geobacter sulfurreducens pilus and higher conductivity of its mutants reflected that biological synthesis can be utilized to improve the properties of electrically conductive pili. However, the structural basis for diverse conductivities of nanowires remains uncertain. Here, the impacts of point mutations on the flexibility and stability of pilins were investigated based on molecular dynamics simulations. Structures of the G. sulfurreducens pilus and its mutants were constructed by Rosetta. Details of the structure (i.e., electrostatic properties, helical parameters, residue interaction network, distances between amino acids, and salt bridges) were analyzed by PDB2PQR, Rosetta, RING, PyMOL, and VMD, respectively. Changes in stability, flexibility, residue interaction, and electrostatic properties of subunits directly caused wild-type pilin and its mutants assemble different structures of G. sulfurreducens pili. By comparing the structures of pili with different conductivities, the mechanism by which the G. sulfurreducens pilus transfers electron along pili was attributed, at least in part, to the density of aromatic rings, the distances between neighboring aromatic rings, and the local electrostatic environment around aromatic contacts. These results provide new insight into the potential for the biological synthesis of highly electrically conductive, nontoxic nanowires.
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20
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Zhou G, Yao Y, Lu Z, Yang X, Han J, Wang G, Rao X, Li P, Liu Q, Song Q. Hydrogen-peroxide-modified egg albumen for transparent and flexible resistive switching memory. NANOTECHNOLOGY 2017; 28:425202. [PMID: 28767040 DOI: 10.1088/1361-6528/aa8397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Egg albumen is modified by hydrogen peroxide with concentrations of 5%, 10%, 15% and 30% at room temperature. Compared with devices without modification, a memory cell of Ag/10% H2O2-egg albumen/indium tin oxide exhibits obviously enhanced resistive switching memory behavior with a resistance ratio of 104, self-healing switching endurance for 900 cycles and a prolonged retention time for a 104 s @ 200 mV reading voltage after being bent 103 times. The breakage of massive protein chains occurs followed by the recombination of new protein chain networks due to the oxidation of amidogen and the synthesis of disulfide during the hydrogen peroxide modifying egg albumen. Ions such as Fe3+, Na+, K+, which are surrounded by protein chains, are exposed to the outside of protein chains to generate a series of traps during the egg albumen degeneration process. According to the fitting results of the double logarithm I-V curves and the current-sensing atomic force microscopy (CS-AFM) images of the ON and OFF states, the charge transfer from one trap center to its neighboring trap center is responsible for the resistive switching memory phenomena. The results of our work indicate that hydrogen- peroxide-modified egg albumen could open up a new avenue of biomaterial application in nanoelectronic systems.
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Affiliation(s)
- Guangdong Zhou
- Institute for Clean Energy and Advanced Materials (ICEAM), Southwest University, Chongqing 400715, People's Republic of China
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21
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Michelson K, Sanford RA, Valocchi AJ, Werth CJ. Nanowires of Geobacter sulfurreducens Require Redox Cofactors to Reduce Metals in Pore Spaces Too Small for Cell Passage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11660-11668. [PMID: 28929755 DOI: 10.1021/acs.est.7b02531] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Members of the Geobacteraceae family are ubiquitous metal reducers that utilize conductive "nanowires" to reduce Mn(IV) and Fe(III) oxides in anaerobic sediments. However, it is not currently known if and to what extent the Mn(IV) and Fe(III) oxides in soil grains and low permeability sediments that are sequestered in pore spaces too small for cell passage can be reduced by long-range extracellular electron transport via Geobacter nanowires, and what mechanisms control this reduction. We developed a microfluidic reactor that physically separates Geobacter sulfurreducens from the Mn(IV) mineral birnessite by a 1.4 μm thick wall containing <200 nm pores. Using optical microscopy and Raman spectroscopy, we show that birnessite can be reduced up to 15 μm away from cell bodies, similar to the reported length of Geobacter nanowires. Reduction across the nanoporous wall required reducing conditions, provided by Escherichia coli, and an exogenous supply of riboflavin. Our results discount electron shuttling by dissolved flavins, and instead support their role as bound redox cofactors in electron transport from nanowires to metal oxides. We also show that upon addition of a soluble electron shuttle (i.e., AQDS), reduction extends beyond the reported nanowire length up to 40 μm into a layer of birnessite.
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Affiliation(s)
- Kyle Michelson
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign , 1301 West Green Street, Urbana, Illinois 61801, United States
| | - Albert J Valocchi
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Charles J Werth
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
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22
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Seviour TW, Hinks J. Bucking the current trend in bioelectrochemical systems: a case for bioelectroanalytics. Crit Rev Biotechnol 2017; 38:634-646. [DOI: 10.1080/07388551.2017.1380599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Thomas William Seviour
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
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23
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Shu C, Xiao K, Cao C, Ding D, Sun X. Predicting and Interpreting the Structure of Type IV Pilus of Electricigens by Molecular Dynamics Simulations. Molecules 2017; 22:E1342. [PMID: 28805699 PMCID: PMC6152092 DOI: 10.3390/molecules22081342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022] Open
Abstract
Nanowires that transfer electrons to extracellular acceptors are important in organic matter degradation and nutrient cycling in the environment. Geobacter pili of the group of Type IV pilus are regarded as nanowire-like biological structures. However, determination of the structure of pili remains challenging due to the insolubility of monomers, presence of surface appendages, heterogeneity of the assembly, and low-resolution of electron microscopy techniques. Our previous study provided a method to predict structures for Type IV pili. In this work, we improved on our previous method using molecular dynamics simulations to optimize structures of Neisseria gonorrhoeae (GC), Neisseria meningitidis and Geobacter uraniireducens pilus. Comparison between the predicted structures for GC and Neisseria meningitidis pilus and their native structures revealed that proposed method could predict Type IV pilus successfully. According to the predicted structures, the structural basis for conductivity in G.uraniireducens pili was attributed to the three N-terminal aromatic amino acids. The aromatics were interspersed within the regions of charged amino acids, which may influence the configuration of the aromatic contacts and the rate of electron transfer. These results will supplement experimental research into the mechanism of long-rang electron transport along pili of electricigens.
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Affiliation(s)
- Chuanjun Shu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, SoutheastUniversity, Nanjing 210096, China.
| | - Ke Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, SoutheastUniversity, Nanjing 210096, China.
| | - Changchang Cao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, SoutheastUniversity, Nanjing 210096, China.
| | - Dewu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, SoutheastUniversity, Nanjing 210096, China.
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, SoutheastUniversity, Nanjing 210096, China.
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24
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Li C, Lesnik KL, Liu H. Stay connected: Electrical conductivity of microbial aggregates. Biotechnol Adv 2017; 35:669-680. [PMID: 28768145 DOI: 10.1016/j.biotechadv.2017.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/25/2017] [Accepted: 07/27/2017] [Indexed: 01/01/2023]
Abstract
The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers.
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Affiliation(s)
- Cheng Li
- Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA
| | - Keaton Larson Lesnik
- Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA
| | - Hong Liu
- Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA.
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25
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Ing NL, Nusca TD, Hochbaum AI. Geobacter sulfurreducenspili support ohmic electronic conduction in aqueous solution. Phys Chem Chem Phys 2017; 19:21791-21799. [DOI: 10.1039/c7cp03651e] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Solid-state and electrochemical observations of ohmic conductivity in purifiedGeobacter sulfurreducenspili.
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Affiliation(s)
- Nicole L. Ing
- Department of Chemical Engineering and Materials Science
- University of California
- Irvine
- Irvine
- USA
| | - Tyler D. Nusca
- Department of Chemical Engineering and Materials Science
- University of California
- Irvine
- Irvine
- USA
| | - Allon I. Hochbaum
- Department of Chemical Engineering and Materials Science
- University of California
- Irvine
- Irvine
- USA
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26
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Shu C, Xiao K, Yan Q, Sun X. Comparative Analysis of Type IV Pilin in Desulfuromonadales. Front Microbiol 2016; 7:2080. [PMID: 28066394 PMCID: PMC5174107 DOI: 10.3389/fmicb.2016.02080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
During anaerobic respiration, the bacteria Geobacter sulfurreducens can transfer electrons to extracellular electron accepters through its pilus. G. sulfurreducens pili have been reported to have metallic-like conductivity that is similar to doped organic semiconductors. To study the characteristics and origin of conductive pilin proteins found in the pilus structure, their genetic, structural, and phylogenetic properties were analyzed. The genetic relationships, and conserved structures and sequences that were obtained were used to predict the evolution of the pilins. Homologous genes that encode conductive pilin were found using PilFind and Cluster. Sequence characteristics and protein tertiary structures were analyzed with MAFFT and QUARK, respectively. The origin of conductive pilins was explored by building a phylogenetic tree. Truncation is a characteristic of conductive pilin. The structures of truncated pilins and their accompanying proteins were found to be similar to the N-terminal and C-terminal ends of full-length pilins respectively. The emergence of the truncated pilins can probably be ascribed to the evolutionary pressure of their extracellular electron transporting function. Genes encoding truncated pilins and proteins similar to the C-terminal of full-length pilins, which contain a group of consecutive anti-parallel beta-sheets, are adjacent in bacterial genomes. According to the genetic, structure, and phylogenetic analyses performed in this study, we inferred that the truncated pilins and their accompanying proteins probably evolved from full-length pilins by gene fission through duplication, degeneration, and separation. These findings provide new insights about the molecular mechanisms involved in long-range electron transport along the conductive pili of Geobacter species.
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Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China
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27
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28
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Extracellular electron transfer mechanisms between microorganisms and minerals. Nat Rev Microbiol 2016; 14:651-62. [DOI: 10.1038/nrmicro.2016.93] [Citation(s) in RCA: 850] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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29
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Xiao K, Malvankar NS, Shu C, Martz E, Lovley DR, Sun X. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili. Sci Rep 2016; 6:23385. [PMID: 27001169 PMCID: PMC4802205 DOI: 10.1038/srep23385] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/03/2016] [Indexed: 12/18/2022] Open
Abstract
The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.
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Affiliation(s)
- Ke Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Nikhil S Malvankar
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Chuanjun Shu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Eric Martz
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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30
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Adhikari RY, Malvankar NS, Tuominen MT, Lovley DR. Conductivity of individual Geobacter pili. RSC Adv 2016. [DOI: 10.1039/c5ra28092c] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Measurements of the conductivity of hydrated individual pili of Geobacter sulfurreducens that were not subjected to chemical fixation revealed conductivity along cytochrome-free regions comparable to conducting organic polymer nanowires of similar diameter.
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Affiliation(s)
| | - Nikhil S. Malvankar
- Department of Physics
- University of Massachusetts
- Amherst
- USA
- Department of Microbiology
| | | | - Derek R. Lovley
- Department of Microbiology
- University of Massachusetts
- Amherst
- USA
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31
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Phan H, Yates MD, Kirchhofer ND, Bazan GC, Tender LM, Nguyen TQ. Biofilm as a redox conductor: a systematic study of the moisture and temperature dependence of its electrical properties. Phys Chem Chem Phys 2016; 18:17815-21. [DOI: 10.1039/c6cp03583c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The variation of the conductivity of a Geobacter biofilm and an osmium redox complex film with temperature has either a positive or negative correlation depending on how the ambient moisture is regulated.
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Affiliation(s)
- Hung Phan
- Department of Chemistry and Biochemistry
- University of California Santa Barbara
- USA
- Center for Polymers and Organic Solids (CPOS)
- University of California Santa Barbara
| | - Matthew D. Yates
- National Research Council
- Washington DC 20007
- USA
- Center for Bio/Molecular Science and Engineering
- Navy Research Laboratory
| | | | - Guillermo C. Bazan
- Department of Chemistry and Biochemistry
- University of California Santa Barbara
- USA
- Center for Polymers and Organic Solids (CPOS)
- University of California Santa Barbara
| | - Leonard M. Tender
- Center for Bio/Molecular Science and Engineering
- Navy Research Laboratory
- Washington
- USA
| | - Thuc-Quyen Nguyen
- Department of Chemistry and Biochemistry
- University of California Santa Barbara
- USA
- Center for Polymers and Organic Solids (CPOS)
- University of California Santa Barbara
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32
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Lebedev N, Mahmud S, Griva I, Blom A, Tender LM. On the electron transfer through Geobacter sulfurreducens
PilA protein. ACTA ACUST UNITED AC 2015. [DOI: 10.1002/polb.23809] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Nikolai Lebedev
- Center for Bio-Molecular Science and Engineering; Naval Research Laboratory; Washington DC 20375
| | - Syed Mahmud
- Center for Bio-Molecular Science and Engineering; Naval Research Laboratory; Washington DC 20375
| | - Igor Griva
- Department of Mathematical Sciences and Computational Material Science Center George Mason University; Fairfax Virginia 22030
| | - Anders Blom
- QuantumWise A/S; Lersø Parkallé 107 Copenhagen DK-2100 Denmark
| | - Leonard M. Tender
- Center for Bio-Molecular Science and Engineering; Naval Research Laboratory; Washington DC 20375
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33
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Feliciano GT, Steidl RJ, Reguera G. Structural and functional insights into the conductive pili of Geobacter sulfurreducens revealed in molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:22217-26. [PMID: 26243427 DOI: 10.1039/c5cp03432a] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Geobacter sulfurreducens (GS) electronically connects with extracellular electron acceptors using conductive protein filaments or pili. To gain insights into their role as biological nanowires, we investigated the structural dynamics of the GS pilus in solution via molecular dynamics simulations. In the model, all of the pilin's aromatics clustered as a right-handed helical band along the pilus, maintaining inter-aromatic distances and dimer configurations optimal for multistep hopping. The aromatics were interspersed within the regions of highest negative potential, which influenced the type and configuration of the aromatic contacts and the rates of electron transfer. Small foci of positive potential were also present but were neutralized within uncharged regions, thus minimizing charge trapping. Consistent with the model predictions, mutant strains with reduced aromatic contacts or negative potentials had defects in pili functions such as the reduction of Fe(III) oxides and electrodes. The results therefore support the notion of a pilus fiber evolved to function as an electronic conduit between the cell and extracellular electron acceptors.
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Affiliation(s)
- G T Feliciano
- Departamento de Físico-Química, Instituto de Quimica, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Nanobionics Group, Sao Paulo, Araraquara, Brazil
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34
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Semenec L, E Franks A. Delving through electrogenic biofilms: from anodes to cathodes to microbes. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.222] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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