1
|
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.
Collapse
|
2
|
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.
Collapse
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,
| |
Collapse
|
3
|
|
4
|
Structure of Geobacter pili reveals secretory rather than nanowire behaviour. Nature 2021; 597:430-434. [PMID: 34471289 PMCID: PMC9127704 DOI: 10.1038/s41586-021-03857-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
Extracellular electron transfer by Geobacter species through surface appendages known as microbial nanowires1 is important in a range of globally important environmental phenomena2, as well as for applications in bio-remediation, bioenergy, biofuels and bioelectronics. Since 2005, these nanowires have been thought to be type 4 pili composed solely of the PilA-N protein1. However, previous structural analyses have demonstrated that, during extracellular electron transfer, cells do not produce pili but rather nanowires made up of the cytochromes OmcS2,3 and OmcZ4. Here we show that Geobacter sulfurreducens binds PilA-N to PilA-C to assemble heterodimeric pili, which remain periplasmic under nanowire-producing conditions that require extracellular electron transfer5. Cryo-electron microscopy revealed that C-terminal residues of PilA-N stabilize its copolymerization with PilA-C (to form PilA-N-C) through electrostatic and hydrophobic interactions that position PilA-C along the outer surface of the filament. PilA-N-C filaments lack π-stacking of aromatic side chains and show a conductivity that is 20,000-fold lower than that of OmcZ nanowires. In contrast with surface-displayed type 4 pili, PilA-N-C filaments show structure, function and localization akin to those of type 2 secretion pseudopili6. The secretion of OmcS and OmcZ nanowires is lost when pilA-N is deleted and restored when PilA-N-C filaments are reconstituted. The substitution of pilA-N with the type 4 pili of other microorganisms also causes a loss of secretion of OmcZ nanowires. As all major phyla of prokaryotes use systems similar to type 4 pili, this nanowire translocation machinery may have a widespread effect in identifying the evolution and prevalence of diverse electron-transferring microorganisms and in determining nanowire assembly architecture for designing synthetic protein nanowires.
Collapse
|
5
|
Mezzina Freitas LP, Feliciano GT. Atomic and Electronic Structure of Pilus from Geobacter sulfurreducens through QM/MM Calculations: Evidence for Hole Transfer in Aromatic Residues. J Phys Chem B 2021; 125:8305-8312. [PMID: 34292748 DOI: 10.1021/acs.jpcb.1c01185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long-range electron transport has been widely and experimentally reported in Geobacter sulfurreducens pilus protein. However, a better understanding of the still undefined molecular arrangement can bring to light the role of key residues in this phenomenon. We propose a theoretical investigation of the electronic structure of aromatic residue groups in the protein through a classical molecular dynamics (MD) simulation, followed by a quantum mechanics/molecular mechanics (QM/MM) electronic study of different frames sampled from MD trajectories, an electrostatic potential and electron density analysis, an analysis of the density of states, and an investigation of hole formation through Dyson orbital calculations. We observe a highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gap in the ranges of 1.4-2.3 eV and 2.9-3.3 eV and a less intense dipole moment along the aromatic residues in the presence of water in comparison to the system in vacuum. HOMO and LUMO electron densities highlight the occupation of one tyrosine residue in every representation for HOMO and a delocalization along two to three rings for LUMO. The results show how the electronic structure of the aromatic residues is sensitive to the ring arrangement and the surrounding environment. In our study, we observe that slight rearrangements in the fiber geometry can create temporary conditions for hole transfer.
Collapse
Affiliation(s)
- Luis Paulo Mezzina Freitas
- Institute of Chemistry, Department of Engineering, Physics and Mathematics, São Paulo State University, Prof. Francisco Degni 55, 14800-060 Araraquara, Brazil
| | - Gustavo Troiano Feliciano
- Institute of Chemistry, Department of Engineering, Physics and Mathematics, São Paulo State University, Prof. Francisco Degni 55, 14800-060 Araraquara, Brazil
| |
Collapse
|
6
|
Casella A, Panitch A, Leach JK. Endogenous Electric Signaling as a Blueprint for Conductive Materials in Tissue Engineering. Bioelectricity 2021; 3:27-41. [PMID: 34476376 PMCID: PMC8370482 DOI: 10.1089/bioe.2020.0027] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bioelectricity plays an important role in cell behavior and tissue modulation, but is understudied in tissue engineering research. Endogenous electrical signaling arises from the transmembrane potential inherent to all cells and contributes to many cell behaviors, including migration, adhesion, proliferation, and differentiation. Electrical signals are also involved in tissue development and repair. Synthetic and natural conductive materials are under investigation for leveraging endogenous electrical signaling cues in tissue engineering applications due to their ability to direct cell differentiation, aid in maturing electroactive cell types, and promote tissue functionality. In this review, we provide a brief overview of bioelectricity and its impact on cell behavior, report recent literature using conductive materials for tissue engineering, and discuss opportunities within the field to improve experimental design when using conductive substrates.
Collapse
Affiliation(s)
- Alena Casella
- Department of Biomedical Engineering, University of California, Davis, Davis, California, USA
| | - Alyssa Panitch
- Department of Biomedical Engineering, University of California, Davis, Davis, California, USA
- Department of Surgery and UC Davis Health, Sacramento, California, USA
| | - J. Kent Leach
- Department of Biomedical Engineering, University of California, Davis, Davis, California, USA
- Department of Orthopaedic Surgery, UC Davis Health, Sacramento, California, USA
| |
Collapse
|
7
|
Sun YL, Montz BJ, Selhorst R, Tang HY, Zhu J, Nevin KP, Woodard TL, Ribbe AE, Russell TP, Nonnenmann SS, Lovley DR, Emrick T. Solvent-Induced Assembly of Microbial Protein Nanowires into Superstructured Bundles. Biomacromolecules 2021; 22:1305-1311. [PMID: 33591727 DOI: 10.1021/acs.biomac.0c01790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein-based electronic biomaterials represent an attractive alternative to traditional metallic and semiconductor materials due to their environmentally benign production and purification. However, major challenges hindering further development of these materials include (1) limitations associated with processing proteins in organic solvents and (2) difficulties in forming higher-order structures or scaffolds with multilength scale control. This paper addresses both challenges, resulting in the formation of one-dimensional bundles composed of electrically conductive protein nanowires harvested from the microbes Geobacter sulfurreducens and Escherichia coli. Processing these bionanowires from common organic solvents, such as hexane, cyclohexane, and DMF, enabled the production of multilength scale structures composed of distinctly visible pili. Transmission electron microscopy revealed striking images of bundled protein nanowires up to 10 μm in length and with widths ranging from 50-500 nm (representing assembly of tens to hundreds of nanowires). Conductive atomic force microscopy confirmed the presence of an appreciable nanowire conductivity in their bundled state. These results greatly expand the possibilities for fabricating a diverse array of protein nanowire-based electronic device architectures.
Collapse
Affiliation(s)
- Yun-Lu Sun
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Brian J Montz
- Department of Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Ryan Selhorst
- Department of Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Hai-Yan Tang
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Jiaxin Zhu
- Department of Mechanical and Industrial Engineering, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Kelly P Nevin
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Trevor L Woodard
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Alexander E Ribbe
- Department of Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Thomas P Russell
- Department of Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Stephen S Nonnenmann
- Department of Mechanical and Industrial Engineering, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| | - Todd Emrick
- Department of Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst, Massachusetts01003, United States
| |
Collapse
|
8
|
Derr JB, Tamayo J, Clark JA, Morales M, Mayther MF, Espinoza EM, Rybicka-Jasińska K, Vullev VI. Multifaceted aspects of charge transfer. Phys Chem Chem Phys 2020; 22:21583-21629. [PMID: 32785306 PMCID: PMC7544685 DOI: 10.1039/d0cp01556c] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.
Collapse
Affiliation(s)
- James B Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Lovley DR, Holmes DE. Protein Nanowires: the Electrification of the Microbial World and Maybe Our Own. J Bacteriol 2020; 202:e00331-20. [PMID: 32747429 PMCID: PMC7515249 DOI: 10.1128/jb.00331-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Electrically conductive protein nanowires appear to be widespread in the microbial world and are a revolutionary "green" material for the fabrication of electronic devices. Electrically conductive pili (e-pili) assembled from type IV pilin monomers have independently evolved multiple times in microbial history as have electrically conductive archaella (e-archaella) assembled from homologous archaellin monomers. A role for e-pili in long-range (micrometer) extracellular electron transport has been demonstrated in some microbes. The surprising finding of e-pili in syntrophic bacteria and the role of e-pili as conduits for direct interspecies electron transfer have necessitated a reassessment of routes for electron flux in important methanogenic environments, such as anaerobic digesters and terrestrial wetlands. Pilin monomers similar to those found in e-pili may also be a major building block of the conductive "cables" that transport electrons over centimeter distances through continuous filaments of cable bacteria consisting of a thousand cells or more. Protein nanowires harvested from microbes have many functional and sustainability advantages over traditional nanowire materials and have already yielded novel electronic devices for sustainable electricity production, neuromorphic memory, and sensing. e-pili can be mass produced with an Escherichia coli chassis, providing a ready source of material for electronics as well as for studies on the basic mechanisms for long-range electron transport along protein nanowires. Continued exploration is required to better understand the electrification of microbial communities with microbial nanowires and to expand the "green toolbox" of sustainable materials for wiring and powering the emerging "Internet of things."
Collapse
Affiliation(s)
- Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| |
Collapse
|
10
|
Abstract
Memristive devices are promising candidates to emulate biological computing. However, the typical switching voltages (0.2-2 V) in previously described devices are much higher than the amplitude in biological counterparts. Here we demonstrate a type of diffusive memristor, fabricated from the protein nanowires harvested from the bacterium Geobacter sulfurreducens, that functions at the biological voltages of 40-100 mV. Memristive function at biological voltages is possible because the protein nanowires catalyze metallization. Artificial neurons built from these memristors not only function at biological action potentials (e.g., 100 mV, 1 ms) but also exhibit temporal integration close to that in biological neurons. The potential of using the memristor to directly process biosensing signals is also demonstrated. Designing energy efficient systems capable to directly process signals at biological voltages remains a challenge. Here, the authors propose a bio-compatible memristor device based on protein-nanowire dielectric, harvested from the bacterium Geobactor sulfurreducens, working at biological voltages.
Collapse
|
11
|
Liu X, Gao H, Ward JE, Liu X, Yin B, Fu T, Chen J, Lovley DR, Yao J. Power generation from ambient humidity using protein nanowires. Nature 2020; 578:550-554. [DOI: 10.1038/s41586-020-2010-9] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/14/2019] [Indexed: 01/30/2023]
|
12
|
Bray MS, Wu J, Padilla CC, Stewart FJ, Fowle DA, Henny C, Simister RL, Thompson KJ, Crowe SA, Glass JB. Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:49-57. [PMID: 31701641 PMCID: PMC7779115 DOI: 10.1111/1758-2229.12809] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/14/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Electroactive type IV pili, or e-pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e-pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22-aa aromatic gaps and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e-pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e-pilins were diverse in length and phylogeny, and included truncated e-pilins in Geobacter spp., as well as longer putative e-pilins in Fe(II)-oxidizing Betaproteobacteria and Zetaproteobacteria.
Collapse
Affiliation(s)
- Marcus S. Bray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jieying Wu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cory C. Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David A. Fowle
- Department of Geology, University of Kansas, Lawrence, KS, USA
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Rachel L. Simister
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Katharine J. Thompson
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Sean A. Crowe
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Division of Earth and Planetary Sciences, School of Biological Sciences, and Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Jennifer B. Glass
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Reguera G. Microbial nanowires and electroactive biofilms. FEMS Microbiol Ecol 2019; 94:5000162. [PMID: 29931163 DOI: 10.1093/femsec/fiy086] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022] Open
Abstract
Geobacter bacteria are the only microorganisms known to produce conductive appendages or pili to electronically connect cells to extracellular electron acceptors such as iron oxide minerals and uranium. The conductive pili also promote cell-cell aggregation and the formation of electroactive biofilms. The hallmark of these electroactive biofilms is electronic heterogeneity, mediated by coordinated interactions between the conductive pili and matrix-associated cytochromes. Collectively, the matrix-associated electron carriers discharge respiratory electrons from cells in multilayered biofilms to electron-accepting surfaces such as iron oxide coatings and electrodes poised at a metabolically oxidizable potential. The presence of pilus nanowires in the electroactive biofilms also promotes the immobilization and reduction of soluble metals, even when present at toxic concentrations. This review summarizes current knowledge about the composition of the electroactive biofilm matrix and the mechanisms that allow the wired Geobacter biofilms to generate electrical currents and participate in metal redox transformations.
Collapse
Affiliation(s)
- Gemma Reguera
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
16
|
Ing NL, El-Naggar MY, Hochbaum AI. Going the Distance: Long-Range Conductivity in Protein and Peptide Bioelectronic Materials. J Phys Chem B 2018; 122:10403-10423. [DOI: 10.1021/acs.jpcb.8b07431] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Reguera G. Harnessing the power of microbial nanowires. Microb Biotechnol 2018; 11:979-994. [PMID: 29806247 PMCID: PMC6201914 DOI: 10.1111/1751-7915.13280] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/13/2018] [Accepted: 04/22/2018] [Indexed: 12/13/2022] Open
Abstract
The reduction of iron oxide minerals and uranium in model metal reducers in the genus Geobacter is mediated by conductive pili composed primarily of a structurally divergent pilin peptide that is otherwise recognized, processed and assembled in the inner membrane by a conserved Type IVa pilus apparatus. Electronic coupling among the peptides is promoted upon assembly, allowing the discharge of respiratory electrons at rates that greatly exceed the rates of cellular respiration. Harnessing the unique properties of these conductive appendages and their peptide building blocks in metal bioremediation will require understanding of how the pilins assemble to form a protein nanowire with specialized sites for metal immobilization. Also important are insights into how cells assemble the pili to make an electroactive matrix and grow on electrodes as biofilms that harvest electrical currents from the oxidation of waste organic substrates. Genetic engineering shows promise to modulate the properties of the peptide building blocks, protein nanowires and current‐harvesting biofilms for various applications. This minireview discusses what is known about the pilus material properties and reactions they catalyse and how this information can be harnessed in nanotechnology, bioremediation and bioenergy applications.
Collapse
Affiliation(s)
- Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd., Rm. 6190, East Lansing, MI, 48824, USA
| |
Collapse
|
19
|
Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
Collapse
Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
| | | | | | | | | | | |
Collapse
|
20
|
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.
Collapse
|
21
|
Dhar BR, Sim J, Ryu H, Ren H, Santo Domingo JW, Chae J, Lee HS. Microbial activity influences electrical conductivity of biofilm anode. WATER RESEARCH 2017; 127:230-238. [PMID: 29055828 PMCID: PMC7321815 DOI: 10.1016/j.watres.2017.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 05/14/2023]
Abstract
This study assessed the conductivity of a Geobacter-enriched biofilm anode in a microbial electrochemical cell (MxC) equipped with two gold anodes (25 mM acetate medium), as different proton gradients were built throughout the biofilm. There was no pH gradient across the biofilm anode at 100 mM phosphate buffer (current density 2.38 A/m2) and biofilm conductivity (Kbio) was as high as 0.87 mS/cm. In comparison, an inner biofilm became acidic at 2.5 mM phosphate buffer in which dead cells were accumulated at ∼80 μm of the inner biofilm anode. At this low phosphate buffer, Kbio significantly decreased by 0.27 mS/cm, together with declined current density of 0.64 A/m2. This work demonstrates that biofilm conductivity depends on the composition of live and dead cells in the conductive biofilm anode.
Collapse
Affiliation(s)
- Bipro Ranjan Dhar
- Civil and Environmental Engineering, University of Alberta, 9211-116 Street NW, Edmonton, Alberta, T6G 1H9, Canada; Civil and Environmental Engineering, University of Waterloo, 200 University Avenue, West Waterloo, Ontario, N2L 3G, Canada.
| | - Junyoung Sim
- Civil and Environmental Engineering, University of Waterloo, 200 University Avenue, West Waterloo, Ontario, N2L 3G, Canada.
| | - Hodon Ryu
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, 26 W. Martin Luther King Drive, Cincinnati, OH 45268, USA.
| | - Hao Ren
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, 85287, USA.
| | - Jorge W Santo Domingo
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, 26 W. Martin Luther King Drive, Cincinnati, OH 45268, USA.
| | - Junseok Chae
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, 85287, USA.
| | - Hyung-Sool Lee
- Civil and Environmental Engineering, University of Waterloo, 200 University Avenue, West Waterloo, Ontario, N2L 3G, Canada.
| |
Collapse
|
22
|
Affiliation(s)
- Derek R. Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| |
Collapse
|
23
|
Electrically conductive pili from pilin genes of phylogenetically diverse microorganisms. ISME JOURNAL 2017; 12:48-58. [PMID: 28872631 DOI: 10.1038/ismej.2017.141] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/17/2017] [Accepted: 07/25/2017] [Indexed: 11/08/2022]
Abstract
The possibility that bacteria other than Geobacter species might contain genes for electrically conductive pili (e-pili) was investigated by heterologously expressing pilin genes of interest in Geobacter sulfurreducens. Strains of G. sulfurreducens producing high current densities, which are only possible with e-pili, were obtained with pilin genes from Flexistipes sinusarabici, Calditerrivibrio nitroreducens and Desulfurivibrio alkaliphilus. The conductance of pili from these strains was comparable to native G. sulfurreducens e-pili. The e-pili derived from C. nitroreducens, and D. alkaliphilus pilin genes are the first examples of relatively long (>100 amino acids) pilin monomers assembling into e-pili. The pilin gene from Candidatus Desulfofervidus auxilii did not yield e-pili, suggesting that the hypothesis that this sulfate reducer wires itself with e-pili to methane-oxidizing archaea to enable anaerobic methane oxidation should be reevaluated. A high density of aromatic amino acids and a lack of substantial aromatic-free gaps along the length of long pilins may be important characteristics leading to e-pili. This study demonstrates a simple method to screen pilin genes from difficult-to-culture microorganisms for their potential to yield e-pili; reveals new sources for biologically based electronic materials; and suggests that a wide phylogenetic diversity of microorganisms may use e-pili for extracellular electron exchange.
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
Zhang X, Philips J, Roume H, Guo K, Rabaey K, Prévoteau A. Rapid and Quantitative Assessment of Redox Conduction Across Electroactive Biofilms by using Double Potential Step Chronoamperometry. ChemElectroChem 2017. [DOI: 10.1002/celc.201600853] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xu Zhang
- Center for Microbial Ecology and Technology (cmet); Ghent University; Coupure Links 653 9000 Ghent Belgium
| | - Jo Philips
- Center for Microbial Ecology and Technology (cmet); Ghent University; Coupure Links 653 9000 Ghent Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology (cmet); Ghent University; Coupure Links 653 9000 Ghent Belgium
- MetaGenoPolis; INRA; Université Paris-Saclay Domaine de Vilvert; Bâtiment 325 78350 Jouy-en-Josas France
| | - Kun Guo
- Center for Microbial Ecology and Technology (cmet); Ghent University; Coupure Links 653 9000 Ghent Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (cmet); Ghent University; Coupure Links 653 9000 Ghent Belgium
| | - Antonin Prévoteau
- Center for Microbial Ecology and Technology (cmet); Ghent University; Coupure Links 653 9000 Ghent Belgium
| |
Collapse
|
26
|
Cytochrome OmcZ is essential for the current generation by Geobacter sulfurreducens under low electrode potential. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.01.091] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
27
|
Expressing the Geobacter metallireducens PilA in Geobacter sulfurreducens Yields Pili with Exceptional Conductivity. mBio 2017; 8:mBio.02203-16. [PMID: 28096491 PMCID: PMC5241403 DOI: 10.1128/mbio.02203-16] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The electrically conductive pili (e-pili) of Geobacter sulfurreducens serve as a model for a novel strategy for long-range extracellular electron transfer. e-pili are also a new class of bioelectronic materials. However, the only other Geobacter pili previously studied, which were from G. uraniireducens, were poorly conductive. In order to obtain more information on the range of pili conductivities in Geobacter species, the pili of G. metallireducens were investigated. Heterologously expressing the PilA gene of G. metallireducens in G. sulfurreducens yielded a G. sulfurreducens strain, designated strain MP, that produced abundant pili. Strain MP exhibited phenotypes consistent with the presence of e-pili, such as high rates of Fe(III) oxide reduction and high current densities on graphite anodes. Individual pili prepared at physiologically relevant pH 7 had conductivities of 277 ± 18.9 S/cm (mean ± standard deviation), which is 5,000-fold higher than the conductivity of G. sulfurreducens pili at pH 7 and nearly 1 million-fold higher than the conductivity of G. uraniireducens pili at the same pH. A potential explanation for the higher conductivity of the G. metallireducens pili is their greater density of aromatic amino acids, which are known to be important components in electron transport along the length of the pilus. The G. metallireducens pili represent the most highly conductive pili found to date and suggest strategies for designing synthetic pili with even higher conductivities. IMPORTANCE e-pili are a remarkable electrically conductive material that can be sustainably produced without harsh chemical processes from renewable feedstocks and that contain no toxic components in the final product. Thus, e-pili offer an unprecedented potential for developing novel materials, electronic devices, and sensors for diverse applications with a new "green" technology. Increasing e-pili conductivity will even further expand their potential applications. A proven strategy is to design synthetic e-pili that contain tryptophan, an aromatic amino acid not found in previously studied e-pili. The studies reported here demonstrate that a productive alternative approach is to search more broadly in the microbial world. Surprisingly, even though G. metallireducens and G. sulfurreducens are closely related, the conductivities of their e-pili differ by more than 3 orders of magnitude. The ability to produce e-pili with high conductivity without generating a genetically modified product enhances the attractiveness of this novel electronic material.
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China
| |
Collapse
|
30
|
|
31
|
Lovley DR. Happy together: microbial communities that hook up to swap electrons. ISME JOURNAL 2016; 11:327-336. [PMID: 27801905 DOI: 10.1038/ismej.2016.136] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/29/2016] [Accepted: 09/04/2016] [Indexed: 12/22/2022]
Abstract
The discovery of direct interspecies electron transfer (DIET) and cable bacteria has demonstrated that microbial cells can exchange electrons over long distances (μm-cm) through electrical connections. For example, in the presence of cable bacteria electrons are rapidly transported over centimeter distances, coupling the oxidation of reduced sulfur compounds in anoxic sediments to oxygen reduction in overlying surficial sediments. Bacteria and archaea wired for DIET are found in anaerobic methane-producing and methane-consuming communities. Electrical connections between gut microbes and host cells have also been proposed. Iterative environmental and defined culture studies on methanogenic communities revealed the importance of electrically conductive pili and c-type cytochromes in natural electrical grids, and demonstrated that conductive carbon materials and magnetite can substitute for these biological connectors to facilitate DIET. This understanding has led to strategies to enhance and stabilize anaerobic digestion. Key unknowns warranting further investigation include elucidation of the archaeal electrical connections facilitating DIET-based methane production and consumption; and the mechanisms for long-range electron transfer through cable bacteria. A better understanding of mechanisms for cell-to-cell electron transfer could facilitate the hunt for additional electrically connected microbial communities with omics approaches and could advance spin-off applications such as the development of sustainable bioelectronics materials and bioelectrochemical technologies.
Collapse
Affiliation(s)
- Derek R Lovley
- Department of Microbiology, Morrill IV N Science Center, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|
32
|
Structure of the Neisseria meningitidis Type IV pilus. Nat Commun 2016; 7:13015. [PMID: 27698424 PMCID: PMC5059446 DOI: 10.1038/ncomms13015] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/25/2016] [Indexed: 02/04/2023] Open
Abstract
Neisseria meningitidis use Type IV pili (T4P) to adhere to endothelial cells and breach the blood brain barrier, causing cause fatal meningitis. T4P are multifunctional polymers of the major pilin protein, which share a conserved hydrophobic N terminus that is a curved extended α-helix, α1, in X-ray crystal structures. Here we report a 1.44 Å crystal structure of the N. meningitidis major pilin PilE and a ∼6 Å cryo-electron microscopy reconstruction of the intact pilus, from which we built an atomic model for the filament. This structure reveals the molecular arrangement of the N-terminal α-helices in the filament core, including a melted central portion of α1 and a bridge of electron density consistent with a predicted salt bridge necessary for pilus assembly. This structure has important implications for understanding pilus biology. Type IV pili are present on a wide range of bacterial pathogens and mediate diverse functions. Here the authors report a high resolution crystal structure of the pilin subunit PilE, and a cryoEM reconstruction of the Type IV pilus filament from N. meningitidis that offer insight into pilus assembly and functions.
Collapse
|
33
|
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]
|