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Zhao J, Wang C, Liu J, Zhang N, Zhao Y, Zhao J, Wang X, Wei W. A biocompatible surface display approach in Shewanella promotes current output efficiency. Biosens Bioelectron 2024; 259:116422. [PMID: 38797034 DOI: 10.1016/j.bios.2024.116422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/04/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
The biology-material hybrid method for chemical-electricity conversion via microbial fuel cells (MFCs) has garnered significant attention in addressing global energy and environmental challenges. However, the efficiency of these systems remains unsatisfactory due to the complex manufacturing process and limited biocompatibility. To overcome these challenges, here, we developed a simple bio-inorganic hybrid system for bioelectricity generation in Shewanella oneidensis (S. oneidensis) MR-1. A biocompatible surface display approach was designed, and silver-binding peptide AgBP2 was expressed on the cell surface. Notably, the engineered Shewanella showed a higher electrochemical sensitivity to Ag+, and a 60 % increase in power density was achieved even at a low concentration of 10 μM Ag+. Further analysis revealed significant upregulations of cell surface negative charge intensity, ATP metabolism, and reducing equivalent (NADH/NAD+) ratio in the engineered S. oneidensis-Ag nanoparticles biohybrid. This work not only provides a novel insight for electrochemical biosensors to detect metal ions, but also offers an alternative biocompatible surface display approach by combining compatible biomaterials with electricity-converting bacteria for advancements in biohybrid MFCs.
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Affiliation(s)
- Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Chen Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jingjing Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Nuo Zhang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yuqin Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China; School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; NJU Xishan Institute of Applied Biotechnology, Wuxi, 214000, China.
| | - Xiuxiu Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China; School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; NJU Xishan Institute of Applied Biotechnology, Wuxi, 214000, China.
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China; NJU Xishan Institute of Applied Biotechnology, Wuxi, 214000, China.
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Kelly AR, Glover DJ. Information Transmission through Biotic-Abiotic Interfaces to Restore or Enhance Human Function. ACS APPLIED BIO MATERIALS 2024; 7:3605-3628. [PMID: 38729914 DOI: 10.1021/acsabm.4c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Advancements in reliable information transfer across biotic-abiotic interfaces have enabled the restoration of lost human function. For example, communication between neuronal cells and electrical devices restores the ability to walk to a tetraplegic patient and vision to patients blinded by retinal disease. These impactful medical achievements are aided by tailored biotic-abiotic interfaces that maximize information transfer fidelity by considering the physical properties of the underlying biological and synthetic components. This Review develops a modular framework to define and describe the engineering of biotic and abiotic components as well as the design of interfaces to facilitate biotic-abiotic information transfer using light or electricity. Delineating the properties of the biotic, interface, and abiotic components that enable communication can serve as a guide for future research in this highly interdisciplinary field. Application of synthetic biology to engineer light-sensitive proteins has facilitated the control of neural signaling and the restoration of rudimentary vision after retinal blindness. Electrophysiological methodologies that use brain-computer interfaces and stimulating implants to bypass spinal column injuries have led to the rehabilitation of limb movement and walking ability. Cellular interfacing methodologies and on-chip learning capability have been made possible by organic transistors that mimic the information processing capacity of neurons. The collaboration of molecular biologists, material scientists, and electrical engineers in the emerging field of biotic-abiotic interfacing will lead to the development of prosthetics capable of responding to thought and experiencing touch sensation via direct integration into the human nervous system. Further interdisciplinary research will improve electrical and optical interfacing technologies for the restoration of vision, offering greater visual acuity and potentially color vision in the near future.
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Affiliation(s)
- Alexander R Kelly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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3
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Zhao F, Niman CM, Ostovar G, Chavez MS, Atkinson JT, Bonis BM, Gralnick JA, El-Naggar MY, Boedicker JQ. Red-Light-Induced Genetic System for Control of Extracellular Electron Transfer. ACS Synth Biol 2024; 13:1467-1476. [PMID: 38696739 DOI: 10.1021/acssynbio.3c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported to new host strains. Here, we developed and adapted a red-light-inducible transcription factor for Shewanella oneidensis. This regulatory circuit is based on the iLight optogenetic system, which controls gene expression using red light. A thermodynamic model and promoter engineering were used to adapt this system to achieve differential gene expression in light and dark conditions within a S. oneidensis host strain. We further improved the iLight optogenetic system by adding a repressor to invert the genetic circuit and activate gene expression under red light illumination. The inverted iLight genetic circuit was used to control extracellular electron transfer within S. oneidensis. The ability to use both red- and blue-light-induced optogenetic circuits simultaneously was also demonstrated. Our work expands the synthetic biology capabilities in S. oneidensis, which could facilitate future advances in applications with electrogenic bacteria.
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Affiliation(s)
- Fengjie Zhao
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Ghazaleh Ostovar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08540, United States
| | - Benjamin M Bonis
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - James Q Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
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Wang LC, Chen HK, Wang WJ, Hsu FY, Huang HZ, Kuo RT, Li WP, Tian HK, Yeh CS. Boosting Upconversion Efficiency in Optically Inert Shelled Structures with Electroactive Membrane through Electron Donation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2404120. [PMID: 38727702 DOI: 10.1002/adma.202404120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/05/2024] [Indexed: 05/21/2024]
Abstract
This study innovatively addresses challenges in enhancing upconversion efficiency in lanthanide-based nanoparticles (UCNPs) by exploiting Shewanella oneidensis MR-1, a microorganism capable of extracellular electron transfer. Electroactive membranes, rich in c-type cytochromes, are extracted from bacteria and integrated into membrane-integrated liposomes (MILs), encapsulating core-shelled UCNPs with an optically inactive shell, forming UCNP@MIL constructs. The electroactive membrane, tailored to donate electrons through the inert shell, independently boosts upconversion emission under near-infrared excitation (980 or 1550 nm), bypassing ligand-sensitized UCNPs. The optically inactive shell restricts energy migration, emphasizing electroactive membrane electron donation. Density functional theory calculations elucidate efficient electron transfer due to the electroactive membrane hemes' highest occupied molecular orbital being higher than the valence band maximum of the optically inactive shell, crucial for enhancing energy transfer to emitter ions. The introduction of a SiO2 insulator coating diminishes light enhancement, underscoring the importance of unimpeded electron transfer. Luminescence enhancement remains resilient to variations in emitter or sensitizing ions, highlighting the robustness of the electron transfer-induced phenomenon. However, altering the inert shell material diminishes enhancement, emphasizing the role of electron transfer. This methodology holds significant promise for diverse biological applications. UCNP@MIL offers an advantage in cellular uptake, which proves beneficial for cell imaging.
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Affiliation(s)
- Liu-Chun Wang
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hong-Kai Chen
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wen-Jyun Wang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Fang-Yi Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Hong-Zhang Huang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Rui-Tong Kuo
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wei-Peng Li
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, 701, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Hong-Kang Tian
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
- Hierarchical Green-Energy Materials (Hi-GEM) Research Center, National Cheng Kung University, Tainan, 701, Taiwan
- Program on Smart and Sustainable Manufacturing, Academy of Innovative Semiconductor and Sustainable Manufacturing, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chen-Sheng Yeh
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, 701, Taiwan
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Tokunou Y, Tongu H, Kogure Y, Okamoto A, Toyofuku M, Nomura N. Colony-Based Electrochemistry Reveals Electron Conduction Mechanisms Mediated by Cytochromes and Flavins in Shewanella oneidensis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4670-4679. [PMID: 38411077 DOI: 10.1021/acs.est.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacteria utilize electron conduction in their communities to drive their metabolism, which has led to the development of various environmental technologies, such as electrochemical microbial systems and anaerobic digestion. It is challenging to measure the conductivity among bacterial cells when they hardly form stable biofilms on electrodes. This makes it difficult to identify the biomolecules involved in electron conduction. In the present study, we aimed to identify c-type cytochromes involved in electron conduction in Shewanella oneidensis MR-1 and examine the molecular mechanisms. We established a colony-based bioelectronic system that quantifies bacterial electrical conductivity, without the need for biofilm formation on electrodes. This system enabled the quantification of the conductivity of gene deletion mutants that scarcely form biofilms on electrodes, demonstrating that c-type cytochromes, MtrC and OmcA, are involved in electron conduction. Furthermore, the use of colonies of gene deletion mutants demonstrated that flavins participate in electron conduction by binding to OmcA, providing insight into the electron conduction pathways at the molecular level. Furthermore, phenazine-based electron transfer in Pseudomonas aeruginosa PAO1 and flavin-based electron transfer in Bacillus subtilis 3610 were confirmed, indicating that this colony-based system can be used for various bacteria, including weak electricigens.
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Affiliation(s)
- Yoshihide Tokunou
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Ibaraki 305-0044, Japan
| | - Hiromasa Tongu
- Degree Programs in Life and Earth Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
| | - Yugo Kogure
- Degree Programs in Life and Earth Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
| | - Akihiro Okamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Ibaraki 305-0044, Japan
- School of Chemical Sciences and Engineering, Hokkaido University, 13 Kita, 8 Nishi, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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Naradasu D, Miran W, Okamoto A. Electrochemical Characterization of Two Gut Microbial Strains Cooperatively Promoting Multiple Sclerosis Pathogenesis. Microorganisms 2024; 12:257. [PMID: 38399661 PMCID: PMC10892914 DOI: 10.3390/microorganisms12020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
In this study, we explored the extracellular electron transfer (EET) capabilities of two bacterial strains, OTU0001 and OTU0002, which are demonstrated in biofilm formation in mouse gut and the induction of autoimmune diseases like multiple sclerosis. OTU0002 displayed significant electrogenic behaviour, producing microbial current on an indium tin-doped oxide electrode surface, particularly in the presence of glucose, with a current density of 60 nA/cm2. The presence of cell-surface redox substrate potentially mediating EET was revealed by the redox-based staining method and electrochemical voltammetry assay. However, medium swapping analyses and the addition of flavins, a model redox mediator, suggest that the current production is dominated by soluble endogenous redox substrates in OTU0002. Given redox substrates were detected at the cell surface, the secreted redox molecule may interact with the cellular surface of OTU0002. In contrast to OTU0002, OTU0001 did not exhibit notable electrochemical activity, lacking cell-surface redox molecules. Further, the mixture of the two strains did not increase the current production from OTU0001, suggesting that OTU0001 does not support the EET mechanism of OTU0002. The present work revealed the coexistence of EET and non-EET capable pathogens in multi-species biofilm.
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Affiliation(s)
- Divya Naradasu
- Oral Microbiology, Bristol Dental School, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK;
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
| | - Waheed Miran
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- School of Chemical and Materials Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba 305-0044, Ibaraki, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo 060-8628, Hokkaido, Japan
- Graduate School of Science and Engineering, College of Science and Engineering, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8573, Ibaraki, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Kanagawa, Japan
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8
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van Wonderen JH, Crack JC, Edwards MJ, Clarke TA, Saalbach G, Martins C, Butt JN. Liquid-chromatography mass spectrometry describes post-translational modification of Shewanella outer membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184221. [PMID: 37673350 DOI: 10.1016/j.bbamem.2023.184221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Electrogenic bacteria deliver excess respiratory electrons to externally located metal oxide particles and electrodes. The biochemical basis for this process is arguably best understood for species of Shewanella where the integral membrane complex termed MtrCAB is key to electron transfer across the bacterial outer membranes. A crystal structure was recently resolved for MtrCAB from S. baltica OS185. However, X-ray diffraction did not resolve the N-terminal residues so that the lipidation status of proteins in the mature complex was poorly described. Here we report liquid chromatography mass spectrometry revealing the intact mass values for all three proteins in the MtrCAB complexes purified from Shewanella oneidensis MR-1 and S. baltica OS185. The masses of MtrA and MtrB are consistent with both proteins being processed by Signal Peptidase I and covalent attachment of ten c-type hemes to MtrA. The mass of MtrC is most reasonably interpreted as arising from protein processed by Signal Peptidase II to produce a diacylated lipoprotein containing ten c-type hemes. Our two-step protocol for liquid-chromatography mass spectrometry used a reverse phase column to achieve on-column detergent removal prior to gradient protein resolution and elution. We envisage the method will be capable of simultaneously resolving the intact mass values for multiple proteins in other membrane protein complexes.
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Affiliation(s)
- Jessica H van Wonderen
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Jason C Crack
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Marcus J Edwards
- School of Biological Sciences, University of East Anglia, , Norwich Research Park, Norwich NR4 7TJ, UK; School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Thomas A Clarke
- School of Biological Sciences, University of East Anglia, , Norwich Research Park, Norwich NR4 7TJ, UK
| | - Gerhard Saalbach
- Proteomics Facility, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Carlo Martins
- Proteomics Facility, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Julea N Butt
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; School of Biological Sciences, University of East Anglia, , Norwich Research Park, Norwich NR4 7TJ, UK.
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9
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Carducci NGG, Dey S, Hickey DP. Recent Developments and Applications of Microbial Electrochemical Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:149-183. [PMID: 38273205 DOI: 10.1007/10_2023_236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
This chapter provides a comprehensive overview of microbial electrochemical biosensors, which are a unique class of biosensors that utilize the metabolic activity of microorganisms to convert chemical signals into electrical signals. The principles and mechanisms of these biosensors are discussed, including the different types of microorganisms that can be used. The various applications of microbial electrochemical biosensors in fields such as environmental monitoring, medical diagnostics, and food safety are also explored. The chapter concludes with a discussion of future research directions and potential advancements in the field of microbial electrochemical biosensors.
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Affiliation(s)
- Nunzio Giorgio G Carducci
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Sunanda Dey
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - David P Hickey
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
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10
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Chen JJ. Interfacial Electron Transfer in Chemical and Biological Transformation of Pollutants in Environmental Catalysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21540-21549. [PMID: 38086095 DOI: 10.1021/acs.est.3c05608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Interfacial electron transfer (IET) is essential for chemical and biological transformation of pollutants, operative across diverse lengths and time scales. This Perspective presents an array of multiscale molecular simulation methodologies, supplemented by in situ monitoring and imaging techniques, serving as robust tools to decode IET enhancement mechanisms such as interface molecular modification, catalyst coordination mode, and atomic composition regulation. In addition, three IET-based pollutant transformation systems, an electrocatalytic oxidation system, a bioelectrochemical spatial coupling system, and an enzyme-inspired electrocatalytic system, were developed, demonstrating a high effect in transforming and degrading pollutants. To improve the effectiveness and scalability of IET-based strategies, the refinement of these systems is necessitated through rigorous research and theoretical exploration, particularly in the context of practical wastewater treatment scenarios. Future endeavors aim to elucidate the synergy between biological and chemical modules, edit the environmental functional microorganisms, and harness machine learning for designing advanced environmental catalysts to boost efficiency. This Perspective highlights the powerful potential of IET-focused environmental remediation strategies, emphasizing the critical role of interdisciplinary research in addressing the urgent global challenge of water pollution.
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Affiliation(s)
- Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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11
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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12
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Chen YC, Li YT, Lee CL, Kuo YT, Ho CL, Lin WC, Hsu MC, Long X, Chen JS, Li WP, Su CH, Okamoto A, Yeh CS. Electroactive membrane fusion-liposome for increased electron transfer to enhance radiodynamic therapy. NATURE NANOTECHNOLOGY 2023; 18:1492-1501. [PMID: 37537274 DOI: 10.1038/s41565-023-01476-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
Dynamic therapies have potential in cancer treatments but have limitations in efficiency and penetration depth. Here a membrane-integrated liposome (MIL) is created to coat titanium dioxide (TiO2) nanoparticles to enhance electron transfer and increase radical production under low-dose X-ray irradiation. The exoelectrogenic Shewanella oneidensis MR-1 microorganism presents an innate capability for extracellular electron transfer (EET). An EET-mimicking photocatalytic system is created by coating the TiO2 nanoparticles with the MIL, which significantly enhances superoxide anions generation under low-dose (1 Gy) X-ray activation. The c-type cytochromes-constructed electron channel in the membrane mimics electron transfer to surrounding oxygen. Moreover, the hole transport in the valence band is also observed for water oxidation to produce hydroxyl radicals. The TiO2@MIL system is demonstrated against orthotopic liver tumours in vivo.
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Affiliation(s)
- Ying-Chi Chen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ting Li
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Lai Lee
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yen-Ting Kuo
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Lun Ho
- Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, Japan
| | - Wei-Che Lin
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Ming-Chien Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Xizi Long
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, Tsukuba, Japan
| | - Jia-Sin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Peng Li
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Chia-Hao Su
- Center for General Education, Chang Gung University, Taoyuan, Taiwan.
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, Tsukuba, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
| | - Chen-Sheng Yeh
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan.
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13
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Li L, Liu Z, Meng D, Liu Y, Liu T, Jiang C, Yin H. Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation. mSystems 2023; 8:e0072023. [PMID: 37768051 PMCID: PMC10654088 DOI: 10.1128/msystems.00720-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Tianbo Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Chengying Jiang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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14
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Chen N, Du N, Shen R, He T, Xi J, Tan J, Bian G, Yang Y, Liu T, Tan W, Yu L, Yuan Q. Redox signaling-driven modulation of microbial biosynthesis and biocatalysis. Nat Commun 2023; 14:6800. [PMID: 37884498 PMCID: PMC10603113 DOI: 10.1038/s41467-023-42561-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial communication can drive coordinated functions through sensing, analyzing and processing signal information, playing critical roles in biomanufacturing and life evolution. However, it is still a great challenge to develop effective methods to construct a microbial communication system with coordinated behaviors. Here, we report an electron transfer triggered redox communication network consisting of three building blocks including signal router, optical verifier and bio-actuator for microbial metabolism regulation and coordination. In the redox communication network, the Fe3+/Fe2+ redox signal can be dynamically and reversibly transduced, channeling electrons directly and specifically into bio-actuator cells through iron oxidation pathway. The redox communication network drives gene expression of electron transfer proteins and simultaneously facilitates the critical reducing power regeneration in the bio-actuator, thus enabling regulation of microbial metabolism. In this way, the redox communication system efficiently promotes the biomanufacturing yield and CO2 fixation rate of bio-actuator. Furthermore, the results demonstrate that this redox communication strategy is applicable both in co-culture and microbial consortia. The proposed electron transfer triggered redox communication strategy in this work could provide an approach for reducing power regeneration and metabolic optimization and could offer insights into improving biomanufacturing efficiency.
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Affiliation(s)
- Na Chen
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Na Du
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Ruichen Shen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Tianpei He
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jing Xi
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Guangkai Bian
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, 518055, Shenzhen, P. R. China
| | - Yanbing Yang
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Tiangang Liu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Lilei Yu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China.
| | - Quan Yuan
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China.
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China.
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15
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Fernandes TM, Silva MA, Morgado L, Salgueiro CA. Hemes on a string: insights on the functional mechanisms of PgcA from Geobacter sulfurreducens. J Biol Chem 2023; 299:105167. [PMID: 37595873 PMCID: PMC10570954 DOI: 10.1016/j.jbc.2023.105167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
Microbial extracellular reduction of insoluble compounds requires soluble electron shuttles that diffuse in the environment, freely diffusing cytochromes, or direct contact with cellular conductive appendages that release or harvest electrons to assure a continuous balance between cellular requirements and environmental conditions. In this work, we produced and characterized the three cytochrome domains of PgcA, an extracellular triheme cytochrome that contributes to Fe(III) and Mn(IV) oxides reduction in Geobacter sulfurreducens. The three monoheme domains are structurally homologous, but their heme groups show variable axial coordination and reduction potential values. Electron transfer experiments monitored by NMR and visible spectroscopy show the variable extent to which the domains promiscuously exchange electrons while reducing different electron acceptors. The results suggest that PgcA is part of a new class of cytochromes - microbial heme-tethered redox strings - that use low-complexity protein stretches to bind metals and promote intra- and intermolecular electron transfer events through its cytochrome domains.
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Affiliation(s)
- Tomás M Fernandes
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta A Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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16
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Abstract
Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.
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Affiliation(s)
- J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA; ,
| | - D R Bond
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA; ,
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17
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Grenfell AW, Intile PJ, McFarlane JA, Leung DC, Abdalla K, Wold MC, Kees ED, Gralnick JA. The Outer Membrane Cytochrome OmcA Is Essential for Infection of Shewanella oneidensis by a Zebrafish-Associated Bacteriophage. J Bacteriol 2023; 205:e0046922. [PMID: 37227287 PMCID: PMC10294696 DOI: 10.1128/jb.00469-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
The microbiota-the mixture of microorganisms in the intestinal tract of animals-plays an important role in host biology. Bacteriophages are a prominent, though often overlooked, component of the microbiota. The mechanisms that phage use to infect susceptible cells associated with animal hosts, and the broader role they could play in determining the substituents of the microbiota, are poorly understood. In this study, we isolated a zebrafish-associated bacteriophage, which we named Shewanella phage FishSpeaker. This phage infects Shewanella oneidensis strain MR-1, which cannot colonize zebrafish, but it is unable to infect Shewanella xiamenensis strain FH-1, a strain isolated from the zebrafish gut. Our data suggest that FishSpeaker uses the outer membrane decaheme cytochrome OmcA, which is an accessory component of the extracellular electron transfer (EET) pathway in S. oneidensis, as well as the flagellum to recognize and infect susceptible cells. In a zebrafish colony that lacks detectable FishSpeaker, we found that most Shewanella spp. are sensitive to infection and that some strains are resistant to infection. Our results suggest that phage could act as a selectivity filter for zebrafish-associated Shewanella and show that the EET machinery can be targeted by phage in the environment. IMPORTANCE Phage exert selective pressure on bacteria that influences and shapes the composition of microbial populations. However, there is a lack of native, experimentally tractable systems for studying how phage influence microbial population dynamics in complex communities. Here, we show that a zebrafish-associated phage requires both the outer membrane-associated extracellular electron transfer protein OmcA and the flagellum to infect Shewanella oneidensis strain MR-1. Our results suggest that the newly discovered phage-FishSpeaker-could exert selective pressure that restricts which Shewanella spp. colonize zebrafish. Moreover, the requirement of OmcA for infection by FishSpeaker suggests that the phage preferentially infects cells that are oxygen limited, a condition required for OmcA expression and an ecological feature of the zebrafish gut.
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Affiliation(s)
- Andrew W. Grenfell
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Peter J. Intile
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - John A. McFarlane
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Dani C. Leung
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Khalid Abdalla
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Michael C. Wold
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Eric D. Kees
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
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18
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Baquero DP, Cvirkaite-Krupovic V, Hu SS, Fields JL, Liu X, Rensing C, Egelman EH, Krupovic M, Wang F. Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes. Cell 2023; 186:2853-2864.e8. [PMID: 37290436 PMCID: PMC10330847 DOI: 10.1016/j.cell.2023.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/04/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to numerous potential applications. However, whether other organisms employ similar ECNs for electron transfer remains unknown. Here, using cryoelectron microscopy, we describe the atomic structures of two ECNs from two major orders of hyperthermophilic archaea present in deep-sea hydrothermal vents and terrestrial hot springs. Homologs of Archaeoglobus veneficus ECN are widespread among mesophilic methane-oxidizing Methanoperedenaceae, alkane-degrading Syntrophoarchaeales archaea, and in the recently described megaplasmids called Borgs. The ECN protein subunits lack similarities in their folds; however, they share a common heme arrangement, suggesting an evolutionarily optimized heme packing for efficient electron transfer. The detection of ECNs in archaea suggests that filaments containing closely stacked hemes may be a common and widespread mechanism for long-range electron transfer in both prokaryotic domains of life.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France
| | | | - Shengen Shawn Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Jessie Lynda Fields
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France.
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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19
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Xia Q, Liu R, Chen X, Chen Z, Zhu JJ. In Vivo Voltammetric Imaging of Metal Nanoparticle-Catalyzed Single-Cell Electron Transfer by Fermi Level-Responsive Graphene. RESEARCH (WASHINGTON, D.C.) 2023; 6:0145. [PMID: 37223464 PMCID: PMC10200910 DOI: 10.34133/research.0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/20/2023] [Indexed: 05/25/2023]
Abstract
Metal nanomaterials can facilitate microbial extracellular electron transfer (EET) in the electrochemically active biofilm. However, the role of nanomaterials/bacteria interaction in this process is still unclear. Here, we reported the single-cell voltammetric imaging of Shewanella oneidensis MR-1 at the single-cell level to elucidate the metal-enhanced EET mechanism in vivo by the Fermi level-responsive graphene electrode. Quantified oxidation currents of ~20 fA were observed from single native cells and gold nanoparticle (AuNP)-coated cells in linear sweep voltammetry analysis. On the contrary, the oxidation potential was reduced by up to 100 mV after AuNP modification. It revealed the mechanism of AuNP-catalyzed direct EET decreasing the oxidation barrier between the outer membrane cytochromes and the electrode. Our method offered a promising strategy to understand the nanomaterials/bacteria interaction and guide the rational construction of EET-related microbial fuel cells.
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Affiliation(s)
- Qing Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Rui Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, P. R. China
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20
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Zhang B, Shi S, Tang R, Qiao C, Yang M, You Z, Shao S, Wu D, Yu H, Zhang J, Cao Y, Li F, Song H. Recent advances in enrichment, isolation, and bio-electrochemical activity evaluation of exoelectrogenic microorganisms. Biotechnol Adv 2023; 66:108175. [PMID: 37187358 DOI: 10.1016/j.biotechadv.2023.108175] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Exoelectrogenic microorganisms (EEMs) catalyzed the conversion of chemical energy to electrical energy via extracellular electron transfer (EET) mechanisms, which underlay diverse bio-electrochemical systems (BES) applications in clean energy development, environment and health monitoring, wearable/implantable devices powering, and sustainable chemicals production, thereby attracting increasing attentions from academic and industrial communities in the recent decades. However, knowledge of EEMs is still in its infancy as only ~100 EEMs of bacteria, archaea, and eukaryotes have been identified, motivating the screening and capture of new EEMs. This review presents a systematic summarization on EEM screening technologies in terms of enrichment, isolation, and bio-electrochemical activity evaluation. We first generalize the distribution characteristics of known EEMs, which provide a basis for EEM screening. Then, we summarize EET mechanisms and the principles underlying various technological approaches to the enrichment, isolation, and bio-electrochemical activity of EEMs, in which a comprehensive analysis of the applicability, accuracy, and efficiency of each technology is reviewed. Finally, we provide a future perspective on EEM screening and bio-electrochemical activity evaluation by focusing on (i) novel EET mechanisms for developing the next-generation EEM screening technologies, and (ii) integration of meta-omics approaches and bioinformatics analyses to explore nonculturable EEMs. This review promotes the development of advanced technologies to capture new EEMs.
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Affiliation(s)
- Baocai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Sicheng Shi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Tang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chunxiao Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Meiyi Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shulin Shao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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21
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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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22
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Zhu H, Wang H, Zhang Y, Li Y. Biophotovoltaics: Recent advances and perspectives. Biotechnol Adv 2023; 64:108101. [PMID: 36681132 DOI: 10.1016/j.biotechadv.2023.108101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/02/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
Biophotovoltaics (BPV) is a clean power generation technology that uses self-renewing photosynthetic microorganisms to capture solar energy and generate electrical current. Although the internal quantum efficiency of charge separation in photosynthetic microorganisms is very high, the inefficient electron transfer from photosystems to the extracellular electrodes hampered the electrical outputs of BPV systems. This review summarizes the approaches that have been taken to increase the electrical outputs of BPV systems in recent years. These mainly include redirecting intracellular electron transfer, broadening available photosynthetic microorganisms, reinforcing interfacial electron transfer and design high-performance devices with different configurations. Furthermore, three strategies developed to extract photosynthetic electrons were discussed. Among them, the strategy of using synthetic microbial consortia could circumvent the weak exoelectrogenic activity of photosynthetic microorganisms and the cytotoxicity of exogenous electron mediators, thus show great potential in enhancing the power output and prolonging the lifetime of BPV systems. Lastly, we prospected how to facilitate electron extraction and further improve the performance of BPV systems.
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Affiliation(s)
- Huawei Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Haowei Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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23
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Long X, Tokunou Y, Okamoto A. Mechano-control of Extracellular Electron Transport Rate via Modification of Inter-heme Coupling in Bacterial Surface Cytochrome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7421-7430. [PMID: 37079493 DOI: 10.1021/acs.est.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacterial outer-membrane multi-heme cytochromes (OMCs) mediate extracellular electron transport (EET). While heme alignment dictates the rate of EET, control of inter-heme coupling in a single OMC remains challenging, especially in intact cells. Given that OMCs diffuse and collide without aggregation on the cell surface, the overexpression of OMCs could increase such mechanical stress to impact the OMCs' protein structure. Here, the heme coupling is modified via mechanical interactions among OMCs by controlling their concentrations. Employment of whole-cell circular dichroism (CD) spectra of genetically engineered Escherichia coli reveals that the OMC concentration significantly impacts the molar CD and redox property of OMCs, resulting in a 4-fold change of microbial current production. The overexpression of OMCs increased the conductive current across the biofilm on an interdigitated electrode, indicating that a higher concentration of OMCs causes more lateral inter-protein electron hopping via collision on the cell surface. The present study would open a novel strategy to increase microbial current production by mechanically enhancing the inter-heme coupling.
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Affiliation(s)
- Xizi Long
- School of the Key Laboratory of Typical Environmental Pollution and Health Hazards of Hunan Province, School of Basic Medicine, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Yoshihide Tokunou
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kitaku, Sapporo, Hokkaido 060-8628, Japan
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24
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Lu J, Zhang B, Geng R, Lian G, Dong H. Independent and synergistic bio-reductions of uranium (VI) driven by zerovalent iron in aquifer. WATER RESEARCH 2023; 233:119778. [PMID: 36871383 DOI: 10.1016/j.watres.2023.119778] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Zerovalent iron [Fe(0)] can donate electron for bioprocess, but microbial uranium (VI) [U(VI)] reduction driven by Fe(0) is still poorly understood. In this study, Fe(0) supported U(VI) bio-reduction was steadily achieved in the 160-d continuous-flow biological column. The maximum removal efficiency and capacity of U(VI) were 100% and 46.4 ± 0.52 g/(m3·d) respectively, and the longevity of Fe(0) increased by 3.09 times. U(VI) was reduced to solid UO2, while Fe(0) was finally oxidized to Fe(III). Autotrophic Thiobacillus achieved U(VI) reduction coupled to Fe(0) oxidation, verified by pure culture. H2 produced from Fe(0) corrosion was consumed by autotrophic Clostridium for U(VI) reduction. The detected residual organic intermediates were biosynthesized with energy released from Fe(0) oxidation and utilized by heterotrophic Desulfomicrobium, Bacillus and Pseudomonas to reduce U(VI). Metagenomic analysis found the upregulated genes for U(VI) reduction (e.g., dsrA and dsrB) and Fe(II) oxidation (e.g., CYC1 and mtrA). These functional genes were also transcriptionally expressed. Cytochrome c and glutathione responsible for electron transfer also contributed to U(VI) reduction. This study reveals the independent and synergistic pathways for Fe(0)-dependent U(VI) bio-reduction, providing promising remediation strategy for U(VI)-polluted aquifers.
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Affiliation(s)
- Jianping Lu
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, PR China
| | - Baogang Zhang
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, PR China.
| | - Rongyue Geng
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, PR China
| | - Guoxi Lian
- School of Environment, Beijing Normal University, Beijing 100875, PR China; The Fourth Research and Design Engineering Institute of China National Nuclear Corporation, Shijiazhuang 050021, PR China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science and Resources, China University of Geosciences Beijing, Beijing 100083, PR China
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25
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Wang F, Craig L, Liu X, Rensing C, Egelman EH. Microbial nanowires: type IV pili or cytochrome filaments? Trends Microbiol 2023; 31:384-392. [PMID: 36446702 PMCID: PMC10033339 DOI: 10.1016/j.tim.2022.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
A dynamic field of study has emerged involving long-range electron transport by extracellular filaments in anaerobic bacteria, with Geobacter sulfurreducens being used as a model system. The interest in this topic stems from the potential uses of such systems in bioremediation, energy generation, and new bio-based nanotechnology for electronic devices. These conductive extracellular filaments were originally thought, based upon low-resolution observations of dried samples, to be type IV pili (T4P). However, the recently published atomic structure for the T4P from G. sulfurreducens, obtained by cryo-electron microscopy (cryo-EM), is incompatible with the numerous models that have been put forward for electron conduction. As with all high-resolution structures of T4P, the G. sulfurreducens T4P structure shows a partial melting of the α-helix that substantially impacts the aromatic residue positions such that they are incompatible with conductivity. Furthermore, new work using high-resolution cryo-EM shows that conductive filaments thought to be T4P are actually polymerized cytochromes, with stacked heme groups forming a continuous conductive wire, or extracellular DNA. Recent atomic structures of three different cytochrome filaments from G. sulfurreducens suggest that such polymers evolved independently on multiple occasions. The expectation is that such polymerized cytochromes may be found emanating from other anaerobic organisms.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
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26
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Li F, Tang R, Zhang B, Qiao C, Yu H, Liu Q, Zhang J, Shi L, Song H. Systematic Full-Cycle Engineering Microbial Biofilms to Boost Electricity Production in Shewanella oneidensis. RESEARCH (WASHINGTON, D.C.) 2023; 6:0081. [PMID: 36939407 PMCID: PMC10017123 DOI: 10.34133/research.0081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/31/2023] [Indexed: 02/04/2023]
Abstract
Electroactive biofilm plays a crucial rule in the electron transfer efficiency of microbial electrochemical systems (MES). However, the low ability to form biofilm and the low conductivity of the formed biofilm substantially limit the extracellular electron transfer rate of microbial cells to the electrode surfaces in MES. To promote biofilm formation and enhance biofilm conductivity, we develop synthetic biology approach to systematically engineer Shewanella oneidensis, a model exoelectrogen, via modular manipulation of the full-cycle different stages of biofilm formation, namely, from initial contact, cell adhesion, and biofilm growth stable maturity to cell dispersion. Consequently, the maximum output power density of the engineered biofilm reaches 3.62 ± 0.06 W m-2, 39.3-fold higher than that of the wild-type strain of S. oneidensis, which, to the best our knowledge, is the highest output power density that has ever been reported for the biofilms of the genetically engineered Shewanella strains.
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Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology,
Tianjin University, Tianjin 300072, China
| | - Rui Tang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
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
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology,
Tianjin University, Tianjin 300072, China
| | - Chunxiao Qiao
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
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
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
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
| | - Qijing Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology,
Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
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
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies,
China University of Geoscience in Wuhan, Wuhan, Hubei 430074, China
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering,
Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology,
Tianjin University, Tianjin 300072, China
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27
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Olmsted CN, Ort R, Tran PQ, McDaniel EA, Roden EE, Bond DR, He S, McMahon KD. Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environ Microbiol 2023; 25:705-720. [PMID: 36529539 DOI: 10.1111/1462-2920.16314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET's function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake's bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize predicted EET protein-encoding genes from metagenomics data. We then applied FEET to 36 bog and thermokarst lakes and correlated gene occurrence with environmental data to test our predictions. Our results provide indirect evidence that DOM may participate in bacterioplankton EET. We found a similarly high prevalence of genes encoding putative EET proteins in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We propose that EET and DOM interactions are of ecologically important to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and anoxygenic phototrophs, should be further studied and incorporated into methane emission models of melting permafrost.
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Affiliation(s)
- Charles N Olmsted
- Department of Molecular and Environmental Toxicology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Roger Ort
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Integrative Biology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Daniel R Bond
- Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Shaomei He
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, Wisconsin, USA
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28
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A Cysteine Pair Controls Flavin Reduction by Extracellular Cytochromes during Anoxic/Oxic Environmental Transitions. mBio 2023; 14:e0258922. [PMID: 36645302 PMCID: PMC9973256 DOI: 10.1128/mbio.02589-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Many bacteria of the genus Shewanella are facultative anaerobes able to reduce a broad range of soluble and insoluble substrates, including Fe(III) mineral oxides. Under anoxic conditions, the bacterium Shewanella oneidensis MR-1 uses a porin-cytochrome complex (Mtr) to mediate extracellular electron transfer (EET) across the outer membrane to extracellular substrates. However, it is unclear how EET prevents generating harmful reactive oxygen species (ROS) when exposed to oxic environments. The Mtr complex is expressed under anoxic and oxygen-limited conditions and contains an extracellular MtrC subunit. This has a conserved CX8C motif that inhibits aerobic growth when removed. This inhibition is caused by an increase in ROS that kills the majority of S. oneidensis cells in culture. To better understand this effect, soluble MtrC isoforms with modified CX8C were isolated. These isoforms produced increased concentrations of H2O2 in the presence of flavin mononucleotide (FMN) and greatly increased the affinity between MtrC and FMN. X-ray crystallography revealed that the molecular structure of MtrC isoforms was largely unchanged, while small-angle X-ray scattering suggested that a change in flexibility was responsible for controlling FMN binding. Together, these results reveal that FMN reduction in S. oneidensis MR-1 is controlled by the redox-active disulfide on the cytochrome surface. In the presence of oxygen, the disulfide forms, lowering the affinity for FMN and decreasing the rate of peroxide formation. This cysteine pair consequently allows the cell to respond to changes in oxygen level and survive in a rapidly transitioning environment. IMPORTANCE Bacteria that live at the oxic/anoxic interface have to rapidly adapt to changes in oxygen levels within their environment. The facultative anaerobe Shewanella oneidensis MR-1 can use EET to respire in the absence of oxygen, but on exposure to oxygen, EET could directly reduce extracellular oxygen and generate harmful reactive oxygen species that damage the bacterium. By modifying an extracellular cytochrome called MtrC, we show how preventing a redox-active disulfide from forming causes the production of cytotoxic concentrations of peroxide. The disulfide affects the affinity of MtrC for the redox-active flavin mononucleotide, which is part of the EET pathway. Our results demonstrate how a cysteine pair exposed on the surface controls the path of electron transfer, allowing facultative anaerobic bacteria to rapidly adapt to changes in oxygen concentration at the oxic/anoxic interface.
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29
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525709. [PMID: 36747706 PMCID: PMC9900912 DOI: 10.1101/2023.01.26.525709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups-iron-oxidizing bacteria (FeOB) Gallionella, Sideroxydans, and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c-type cytochromes overall, notably more multiheme c-type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella, Sideroxydans, and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe2+ as well as a range of solid iron or other mineral substrates.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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30
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Tikhonova TV, Osipov EM, Dergousova NI, Boyko KM, Elizarov IM, Gavrilov SN, Khrenova MG, Robb FT, Solovieva AY, Bonch-Osmolovskaya EA, Popov VO. Extracellular Fe(III) reductase structure reveals a modular organization enabling S-layer insertion and electron transfer to insoluble substrates. Structure 2023; 31:174-184.e3. [PMID: 36630959 DOI: 10.1016/j.str.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/16/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023]
Abstract
The thermophilic anaerobic Gram-positive bacterium Carboxydothermus ferrireducens utilizes insoluble Fe(III) oxides as electron acceptors in respiratory processes using an extracellular 11-heme cytochrome c OmhA as a terminal reductase. OmhA is able to transfer electrons to soluble and insoluble Fe(III) compounds, substrates of multiheme oxidoreductases, and soluble electron shuttles. The crystal structure of OmhA at 2.5 Å resolution shows that it consists of two functionally distinct parts: the cytochrome с electron transfer and the S-layer binding domains. Nonaheme C-terminal subdomain of the cytochrome с domain is structurally similar to the extracellular multiheme cytochrome OcwA from the metal-reducing Gram-positive bacterium "Thermincola potens." S-layer binding domain of OmhA is responsible for interaction with the S-layer that surrounds the Carboxydothermus ferrireducens cell envelope. The structural foundations enabling the embedding of extracellular multiheme cytochromes to the S-layer of a Gram-positive-type cell wall and putative electron transfer pathways to insoluble minerals are discussed.
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Affiliation(s)
- Tamara V Tikhonova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation
| | - Evgenii M Osipov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation; Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Natalia I Dergousova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation
| | - Konstantin M Boyko
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation
| | - Ivan M Elizarov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation
| | - Sergey N Gavrilov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation
| | - Maria G Khrenova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation; Department of Chemistry, Lomonosov Moscow State University, 1 Lenin Hills, Building 3, Moscow 119991, Russian Federation
| | - Frank T Robb
- Institute of Marine and Environmental Technology, Center for Environmental Science, University of Maryland, 701 E. Pratt Street, Baltimore, MD 21202, USA
| | - Anastasia Y Solovieva
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation
| | - Elizaveta A Bonch-Osmolovskaya
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation; Department of Biology, Lomonosov Moscow State University, 1 Lenin Hills, Building 12, Moscow 119991, Russian Federation
| | - Vladimir O Popov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation; Department of Biology, Lomonosov Moscow State University, 1 Lenin Hills, Building 12, Moscow 119991, Russian Federation.
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31
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Futera Z, Wu X, Blumberger J. Tunneling-to-Hopping Transition in Multiheme Cytochrome Bioelectronic Junctions. J Phys Chem Lett 2023; 14:445-452. [PMID: 36622944 DOI: 10.1021/acs.jpclett.2c03361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Multiheme cytochromes (MHCs) have attracted much interest for use in nanobioelectronic junctions due to their high electronic conductances. Recent measurements on dry MHC junctions suggested that a coherent tunneling mechanism is operative over surprisingly long long distances (>3 nm), which challenges our understanding of coherent transport phenomena. Here we show that this is due to (i) a low exponential distance decay constant for coherent conduction in MHCs (β = 0.2 Å-1) and (ii) a large density of protein electronic states which prolongs the coherent tunneling regime to distances that exceed those in molecular wires made of small molecules. Incoherent hopping conduction is uncompetitive due to the large energy level offset at the protein-electrode interface. Removing this offset, e.g., by gating, we predict that the transport mechanism crosses over from coherent tunneling to incoherent hopping at a protein size of ∼7 nm, thus enabling transport on the micrometer scale with a shallow polynomial (∼1/r) distance decay.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Xiaojing Wu
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, U.K
| | - Jochen Blumberger
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, U.K
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32
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Wu L, Luo Y, Wang C, Wu S, Zheng Y, Li Z, Cui Z, Liang Y, Zhu S, Shen J, Liu X. Self-Driven Electron Transfer Biomimetic Enzymatic Catalysis of Bismuth-Doped PCN-222 MOF for Rapid Therapy of Bacteria-Infected Wounds. ACS NANO 2023; 17:1448-1463. [PMID: 36622022 DOI: 10.1021/acsnano.2c10203] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In this work, a biomimetic nanozyme catalyst with rapid and efficient self-bacteria-killing and wound-healing performances was synthesized. Through an in situ reduction reaction, a PCN-222 metal organic framework (MOF) was doped with bismuth nanoparticles (Bi NPs) to form Bi-PCN-222, an interfacial Schottky heterojunction biomimetic nanozyme catalyst, which can kill 99.9% of Staphylococcus aureus (S. aureus). The underlying mechanism was that Bi NP doping can endow Bi-PCN-222 MOF with self-driven charge transfer through the Schottky interface and the capability of oxidase-like and peroxidase-like activity, because a large number of free electrons can be captured by surrounding oxygen species to produce radical oxygen species (ROS). Furthermore, once bacteria contact Bi-PCN-222 in a physiological environment, its appropriate redox potential can trigger electron transfer through the electron transport pathway in bacterial membranes and then the interior of the bacteria, which disturbs the bacterial respiration process and subsequent metabolism. Additionally, Bi-PCN-222 can also accelerate tissue regeneration by upregulating fibroblast proliferation and angiogenesis genes (bFGF, VEGF, and HIF-1α), thereby promoting wound healing. This biomimetic enzyme-catalyzed strategy will bring enlightenment to the design of self-bacterial agents for efficient disinfection and tissue reconstruction simultaneously.
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Affiliation(s)
- Lihua Wu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Yue Luo
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Chaofeng Wang
- School of Health Science and Biomedical Engineering, Hebei University of Technology, Tianjin300401, People's Republic of China
| | - Shuilin Wu
- School of Materials Science and Engineering, Peking University, Beijing100871, People's Republic of China
| | - Yufeng Zheng
- School of Materials Science and Engineering, Peking University, Beijing100871, People's Republic of China
| | - Zhaoyang Li
- School of Materials Science & Engineering, The Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin300072, People's Republic of China
| | - Zhenduo Cui
- School of Materials Science & Engineering, The Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin300072, People's Republic of China
| | - Yanqin Liang
- School of Materials Science & Engineering, The Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin300072, People's Republic of China
| | - Shengli Zhu
- School of Materials Science & Engineering, The Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin300072, People's Republic of China
| | - Jie Shen
- Shenzhen Key Laboratory of Spine Surgery, Department of Spine Surgery, Peking University Shenzhen Hospital, Shenzhen516473, People's Republic of China
| | - Xiangmei Liu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan430062, People's Republic of China
- School of Health Science and Biomedical Engineering, Hebei University of Technology, Tianjin300401, People's Republic of China
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33
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Li J, Dong C, Sen B, Lai Q, Gong L, Wang G, Shao Z. Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158714. [PMID: 36113801 DOI: 10.1016/j.scitotenv.2022.158714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea. Yet their role in the mineralization of plant-derived TOM in the deep sea remains largely unknown. Here we isolated Vibrio strains representing dominant members of the enrichments and verified their potential to degrade lignin and xylan. The isolated strains were closely related to Vibrio harveyi, V. alginolyticus, V. diabolicus, and V. parahaemolyticus. Extracellular enzyme assays, and genome and transcriptome analyses revealed diverse peroxidases, including lignin peroxidase (LiP), catalase-peroxidase (KatG), and decolorizing peroxidase (DyP), which played an important role in the depolymerization and oxidation of lignin. Superoxide dismutase was found to likely promote lignin oxidation by supplying H2O2 to LiP, DyP, and KatG. Interestingly, these deep-sea Vibrio strains could oxidize lignin and hydrolyze xylan not only through aerobic pathway, but also through anaerobic pathway. Genome analysis revealed multiple anaerobic respiratory mechanisms, including the reductions of nitrate, arsenate, tetrathionate, and dimethyl sulfoxide. The strains showed the potential to anaerobically reduce sulfite and metal oxides of iron and manganese, in contrast the non-deep-sea Vibrio strains were not retrieved of genes involved in reduction of metal oxides. This is the first report about the lignin oxidation mechanisms in Vibrio and their role in TOM mineralization in anoxic and oxic environments of the marginal sea.
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Affiliation(s)
- Jianyang Li
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China.
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Deciphering Molecular Factors That Affect Electron Transfer at the Cell Surface of Electroactive Bacteria: The Case of OmcA from Shewanella oneidensis MR-1. Microorganisms 2022; 11:microorganisms11010079. [PMID: 36677373 PMCID: PMC9861303 DOI: 10.3390/microorganisms11010079] [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: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Multiheme cytochromes play a central role in extracellular electron transfer, a process that allows microorganisms to sustain their metabolism with external electron acceptors or donors. In Shewanella oneidensis MR-1, the decaheme cytochromes OmcA and MtrC show functional specificity for interaction with soluble and insoluble redox partners. In this work, the capacity of extracellular electron transfer by mutant variants of S. oneidensis MR-1 OmcA was investigated. The results show that amino acid mutations can affect protein stability and alter the redox properties of the protein, without affecting the ability to perform extracellular electron transfer to methyl orange dye or a poised electrode. The results also show that there is a good correlation between the reduction of the dye and the current generated at the electrode for most but not all mutants. This observation opens the door for investigations of the molecular mechanisms of interaction with different electron acceptors to tailor these surface exposed cytochromes towards specific bio-based applications.
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35
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Physiological Benefits of Oxygen-Terminating Extracellular Electron Transfer. mBio 2022; 13:e0195722. [PMID: 36374091 PMCID: PMC9765408 DOI: 10.1128/mbio.01957-22] [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] [Indexed: 11/16/2022] Open
Abstract
Extracellular electron transfer (EET) is a process via which certain microorganisms, such as bacteria, exchange electrons with extracellular materials by creating an electrical link across their membranes. EET has been studied for the reactions on solid materials such as minerals and electrodes with implication in geobiology and biotechnology. EET-capable bacteria exhibit broad phylogenetic diversity, and some are found in environments with various types of electron acceptors/donors not limited to electrodes or minerals. Oxygen has also been shown to serve as the terminal electron acceptor for EET of Pseudomonas aeruginosa and Faecalibacterium prausnitzii. However, the physiological significance of such oxygen-terminating EETs, as well as the mechanisms underlying them, remain unclear. In order to understand the physiological advantage of oxygen-terminating EET and its link with energy metabolism, in this review, we compared oxygen-terminating EET with aerobic respiration, fermentation, and electrode-terminating EET. We also summarized benefits and limitations of oxygen-terminating EET in a biofilm setting, which indicate that EET capability enables bacteria to create a niche in the anoxic zone of aerobic biofilms, thereby remodeling bacterial metabolic activities in biofilms.
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36
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Guo J, Jiang J, Peng Z, Zhong Y, Jiang Y, Jiang Z, Hu Y, Dong Y, Shi L. Global occurrence of the bacteria with capability for extracellular reduction of iodate. Front Microbiol 2022; 13:1070601. [PMID: 36504819 PMCID: PMC9732548 DOI: 10.3389/fmicb.2022.1070601] [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: 10/15/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
The γ-proteobacterium Shewanella oneidensis MR-1 reduces iodate to iodide extracellularly. Both dmsEFAB and mtrCAB gene clusters are involved in extracellular reduction of iodate by S. oneidensis MR-1. DmsEFAB reduces iodate to hypoiodous acid and hydrogen peroxide (H2O2). Subsequently, H2O2 is reduced by MtrCAB to facilitate DmsEFAB-mediated extracellular reduction of iodate. To investigate the distribution of bacteria with the capability for extracellular reduction of iodate, bacterial genomes were systematically searched for both dmsEFAB and mtrCAB gene clusters. The dmsEFAB and mtrCAB gene clusters were found in three Ferrimonas and 26 Shewanella species. Coexistence of both dmsEFAB and mtrCAB gene clusters in these bacteria suggests their potentials for extracellular reduction of iodate. Further analyses demonstrated that these bacteria were isolated from a variety of ecosystems, including the lakes, rivers, and subsurface rocks in East and Southeast Asia, North Africa, and North America. Importantly, most of the bacteria with both dmsEFAB and mtrCAB gene clusters were found in different marine environments, which ranged from the Arctic Ocean to Antarctic coastal marine environments as well as from the Atlantic Ocean to the Indian and Pacific Oceans. Widespread distribution of the bacteria with capability for extracellular reduction of iodate around the world suggests their significant importance in global biogeochemical cycling of iodine. The genetic organization of dmsEFAB and mtrCAB gene clusters also varied substantially. The identified mtrCAB gene clusters often contained additional genes for multiheme c-type cytochromes. The numbers of dmsEFAB gene cluster detected in a given bacterial genome ranged from one to six. In latter, duplications of dmsEFAB gene clusters occurred. These results suggest different paths for these bacteria to acquire their capability for extracellular reduction of iodate.
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Affiliation(s)
- Jinzhi Guo
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Jie Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Zhaofeng Peng
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Zhaofeng Peng,
| | - Yuhong Zhong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, China,*Correspondence: Zhaofeng Peng,
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37
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Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales. mSphere 2022; 7:e0022322. [PMID: 36069437 PMCID: PMC9599434 DOI: 10.1128/msphere.00223-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.
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38
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Piper SEH, Casadevall C, Reisner E, Clarke TA, Jeuken LJC, Gates AJ, Butt JN. Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors. Angew Chem Int Ed Engl 2022; 61:e202210572. [PMID: 35951464 PMCID: PMC9825952 DOI: 10.1002/anie.202210572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 01/11/2023]
Abstract
Nitrous oxide (N2 O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N2 O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N2 O to the climate neutral product N2 . Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N2 O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N2 O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N2 O removal in ambient, aqueous conditions.
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Affiliation(s)
- Samuel E. H. Piper
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Carla Casadevall
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Erwin Reisner
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Thomas A. Clarke
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Lars J. C. Jeuken
- Leiden Institute of ChemistryLeiden UniversityPO Box 95022300 RALeidenThe Netherlands
| | - Andrew J. Gates
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Julea N. Butt
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK,School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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39
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Piper SEH, Casadevall C, Reisner E, Clarke TA, Jeuken LJC, Gates AJ, Butt JN. Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202210572. [PMID: 38529325 PMCID: PMC10962689 DOI: 10.1002/ange.202210572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 11/11/2022]
Abstract
Nitrous oxide (N2O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N2O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N2O to the climate neutral product N2. Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N2O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N2O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N2O removal in ambient, aqueous conditions.
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Affiliation(s)
- Samuel E. H. Piper
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Carla Casadevall
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Erwin Reisner
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Thomas A. Clarke
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Lars J. C. Jeuken
- Leiden Institute of ChemistryLeiden UniversityPO Box 95022300 RALeidenThe Netherlands
| | - Andrew J. Gates
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Julea N. Butt
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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40
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Jain A, Kalb MJ, Gralnick JA. Reconstructing electron transfer components from an Fe(II) oxidizing bacterium. Microbiology (Reading) 2022; 168. [DOI: 10.1099/mic.0.001240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neutrophilic Fe(II) oxidizing bacteria play an important role in biogeochemical processes and have also received attention for multiple technological applications. These micro-organisms are thought to couple their metabolism with extracellular electron transfer (EET) while oxidizing Fe(II) as electron donor outside the cell. Sideroxydans lithotrophicus ES-1 is a freshwater chemolithoautotrophic Fe(II) oxidizing bacterium that is challenging to culture and not yet genetically tractable. Analysis of the S. lithotrophicus ES-1 genome predicts multiple EET pathways, which are proposed to be involved in Fe(II) oxidation, but not yet validated. Here we expressed components of two of the proposed EET pathways, including the Mto and Slit_0867–0870 PCC3 pathways, from S. lithotrophicus ES-1 into
Aeromonas hydrophila
, an established model EET organism. We demonstrate that combinations of putative inner membrane and periplasmic components from the Mto and Slit_0867–0870 PCC3 pathways partially complemented EET activity in
Aeromonas
mutants lacking native components. Our results provide evidence for electron transfer functionality and interactions of inner membrane and periplasmic components from the Mto and Slit_0867–0870 PCC3 pathways. Based on these findings, we suggest that EET in S. lithotrophicus ES-1 could be more complicated than previously considered and raises questions regarding directionality of these electron transfer pathways.
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Affiliation(s)
- Abhiney Jain
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota — Twin Cities, St. Paul, MN 55108, USA
| | - Madison J. Kalb
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota — Twin Cities, St. Paul, MN 55108, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota — Twin Cities, St. Paul, MN 55108, USA
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41
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Yu YY, Zhang Y, Peng L. Investigating the interaction between Shewanella oneidensis and phenazine 1-carboxylic acid in the microbial electrochemical processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156501. [PMID: 35667430 DOI: 10.1016/j.scitotenv.2022.156501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Many exoelectrogens utilize small redox mediators for extracellular electron transfer (EET). Notable examples include Shewanella species, which synthesize flavins, and Pseudomonas species, which produce phenazines. In natural and engineered environments, redox-active metabolites from different organisms coexist. The interaction between Shewanella oneidensis and phenazine 1-carboxylic acid (PCA, a representative phenazine compound) was investigated to demonstrate exoelectrogens utilizing metabolites secreted by other organisms as redox mediators. After 24 h in a reactor with and without added PCA (1 μM), the anodic current generated by Shewanella was 235 ± 11 and 51.7 ± 2.8 μA, respectively. Shewanella produced oxidative current approximately three times as high with medium containing PCA as with medium containing the same concentration of riboflavin. PCA also stimulated inward EET in Shewanella. The strong effect of PCA on EET was attributed to its enrichment at the biofilm/electrode interface. The PCA voltammetric peak heights with a Shewanella bioanode were 25-30 times higher than under abiotic conditions. The electrochemical properties of PCA were also altered by the transition from two-electron to single-electron electrochemistry, which suggests PCA was bound between the electrode and cell surface redox proteins. This behavior would benefit electroactive bacteria, which usually dwell in open systems where mediators are present in low concentrations. Like flavins, PCA can be immobilized under both bioanode and biocathode conditions but not under metabolically inactive conditions. Shewanella rapidly transfers electrons to PCA via its Mtr pathway. Compared with wild-type Shewanella, the PCA reduction ability was decreased in gene knockout mutants lacking Mtr pathway cytochromes, especially in the mutants with severely undermined electrode-reduction capacities. These strains also lost the ability to immobilize PCA, even under current-generating conditions.
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Affiliation(s)
- Yi-Yan Yu
- School of Resources & Environment, Southwest University, Chongqing 400716, PR China
| | - Yong Zhang
- School of Resources & Environment, Southwest University, Chongqing 400716, PR China
| | - Luo Peng
- School of Resources & Environment, Southwest University, Chongqing 400716, PR China.
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42
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Deng Y, Zhang K, Zou J, Li X, Wang Z, Hu C. Electron shuttles enhanced the removal of antibiotics and antibiotic resistance genes in anaerobic systems: A review. Front Microbiol 2022; 13:1004589. [PMID: 36160234 PMCID: PMC9490129 DOI: 10.3389/fmicb.2022.1004589] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
The environmental and epidemiological problems caused by antibiotics and antibiotic resistance genes have attracted a lot of attention. The use of electron shuttles based on enhanced extracellular electron transfer for anaerobic biological treatment to remove widespread antibiotics and antibiotic resistance genes efficiently from wastewater or organic solid waste is a promising technology. This paper reviewed the development of electron shuttles, described the mechanism of action of different electron shuttles and the application of enhanced anaerobic biotreatment with electron shuttles for the removal of antibiotics and related genes. Finally, we discussed the current issues and possible future directions of electron shuttle technology.
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43
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Wang F, Chan CH, Suciu V, Mustafa K, Ammend M, Si D, Hochbaum AI, Egelman EH, Bond DR. Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times. eLife 2022; 11:81551. [PMID: 36062910 PMCID: PMC9473688 DOI: 10.7554/elife.81551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/03/2022] [Indexed: 11/26/2022] Open
Abstract
While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c-type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
| | - Chi Ho Chan
- Department of Plant and MIcrobial Biology, University of Minnesota, St. Paul, United States
| | - Victor Suciu
- Division of Computing and Software Systems, University of Washington Bothell, Bothell, United States
| | - Khawla Mustafa
- Department of Chemistry, University of California, Irvine, Irvine, United States
| | - Madeline Ammend
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States
| | - Dong Si
- Division of Computing and Software Systems, University of Washington Bothell, Bothell, United States
| | - Allon I Hochbaum
- Department of Chemistry, University of California, Irvine, Irvine, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
| | - Daniel R Bond
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States
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44
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Quek G, Vázquez RJ, McCuskey SR, Kundukad B, Bazan GC. Enabling Electron Injection for Microbial Electrosynthesis with n-Type Conjugated Polyelectrolytes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2203480. [PMID: 35835449 DOI: 10.1002/adma.202203480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Microbial electrosynthesis-using renewable electricity to stimulate microbial metabolism-holds the promise of sustainable chemical production. A key limitation hindering performance is slow electron-transfer rates at biotic-abiotic interfaces. Here a new n-type conjugated polyelectrolyte is rationally designed and synthesized and its use is demonstrated as a soft conductive material to encapsulate electroactive bacteria Shewanella oneidensis MR-1. The self-assembled 3D living biocomposite amplifies current uptake from the electrode ≈674-fold over controls with the same initial number of cells, thereby enabling continuous synthesis of succinate from fumarate. Such functionality is a result of the increased number of bacterial cells having intimate electronic communication with the electrode and a higher current uptake per cell. This is underpinned by the molecular design of the polymer to have an n-dopable conjugated backbone for facile reduction by the electrode and zwitterionic side chains for compatibility with aqueous media. Moreover, direct arylation polycondensation is employed instead of the traditional Stille polymerization to avoid non-biocompatible tin by-products. By demonstrating synergy between living cells with n-type organic semiconductor materials, these results provide new strategies for improving the performance of bioelectrosynthesis technologies.
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Affiliation(s)
- Glenn Quek
- Departments of Chemistry and Chemical & Biomolecular Engineering, Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, Singapore, 119077, Singapore
| | - Ricardo Javier Vázquez
- Departments of Chemistry and Chemical & Biomolecular Engineering, Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, Singapore, 119077, Singapore
| | - Samantha R McCuskey
- Departments of Chemistry and Chemical & Biomolecular Engineering, Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, Singapore, 119077, Singapore
| | - Binu Kundukad
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Guillermo C Bazan
- Departments of Chemistry and Chemical & Biomolecular Engineering, Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, Singapore, 119077, Singapore
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45
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Christopher Fry H, Divan R, Liu Y. Designing 1D multiheme peptide amphiphile assemblies reminiscent of natural systems. NANOSCALE 2022; 14:10082-10090. [PMID: 35792094 DOI: 10.1039/d2nr00473a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Protein assemblies that bind and organize ordered arrays of cofactors yield function structures. Multiheme assemblies found in nature yield electronically conductivity 1D nanoscale fibers and are employed in anaerobic respiration. To understand the fundamental characteristics of these organized arrays, the design of peptide amphiphiles that assemble into 1D nanostructures and yield metalloporphyrin binding sites is presented. One challenge with this class of peptide amphiphiles is identifying the correct sequence composition for high affinity binding with high heme density. Here, the peptide c16-AH(Kx)n-CO2H is explored to identify the impact of sequence length (n) and amino acid identity (x = L, I, or F) on binding affinity and midpoint potential. When n = 2, the peptide assembly yields the greatest affinity. The resulting nanoscale assemblies yield ordered arrays of the redox active molecule heme and have potential utility in the development of supramolecular bioelectronic materials useful in sensing as well as the development of enzymatic materials.
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Affiliation(s)
- H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA.
| | - Ralu Divan
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA.
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA.
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46
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Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Nat Microbiol 2022; 7:1291-1300. [PMID: 35798889 PMCID: PMC9357133 DOI: 10.1038/s41564-022-01159-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
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47
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Zhao F, Chavez MS, Naughton KL, Niman CM, Atkinson JT, Gralnick JA, El-Naggar MY, Boedicker JQ. Light-Induced Patterning of Electroactive Bacterial Biofilms. ACS Synth Biol 2022; 11:2327-2338. [PMID: 35731987 DOI: 10.1021/acssynbio.2c00024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electroactive bacterial biofilms can function as living biomaterials that merge the functionality of living cells with electronic components. However, the development of such advanced living electronics has been challenged by the inability to control the geometry of electroactive biofilms relative to solid-state electrodes. Here, we developed a lithographic strategy to pattern conductive biofilms of Shewanella oneidensis by controlling aggregation protein CdrAB expression with a blue light-induced genetic circuit. This controlled deposition enabled S. oneidensis biofilm patterning on transparent electrode surfaces, and electrochemical measurements allowed us to both demonstrate tunable conduction dependent on pattern size and quantify the intrinsic conductivity of the living biofilms. The intrinsic biofilm conductivity measurements enabled us to experimentally confirm predictions based on simulations of a recently proposed collision-exchange electron transport mechanism. Overall, we developed a facile technique for controlling electroactive biofilm formation on electrodes, with implications for both studying and harnessing bioelectronics.
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Affiliation(s)
- Fengjie Zhao
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Kyle L Naughton
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota 55108, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - James Q Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
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48
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Soares R, Costa NL, Paquete CM, Andreini C, Louro RO. A new paradigm of multiheme cytochrome evolution by grafting and pruning protein modules. Mol Biol Evol 2022; 39:6609985. [PMID: 35714268 PMCID: PMC9250108 DOI: 10.1093/molbev/msac139] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multiheme cytochromes play key roles in diverse biogeochemical cycles, but understanding the origin and evolution of these proteins is a challenge due to their ancient origin and complex structure. Up until now, the evolution of multiheme cytochromes composed by multiple redox modules in a single polypeptide chain was proposed to occur by gene fusion events. In this context, the pentaheme nitrite reductase NrfA and the tetraheme cytochrome c554 were previously proposed to be at the origin of the extant octa- and nonaheme cytochrome c involved in metabolic pathways that contribute to the nitrogen, sulfur, and iron biogeochemical cycles by a gene fusion event. Here, we combine structural and character-based phylogenetic analysis with an unbiased root placement method to refine the evolutionary relationships between these multiheme cytochromes. The evidence show that NrfA and cytochrome c554 belong to different clades, which suggests that these two multiheme cytochromes are products of truncation of ancestral octaheme cytochromes related to extant octaheme nitrite reductase and MccA, respectively. From our phylogenetic analysis, the last common ancestor is predicted to be an octaheme cytochrome with nitrite reduction ability. Evolution from this octaheme framework led to the great diversity of extant multiheme cytochromes analyzed here by pruning and grafting of protein modules and hemes. By shedding light into the evolution of multiheme cytochromes that intervene in different biogeochemical cycles, this work contributes to our understanding about the interplay between biology and geochemistry across large time scales in the history of Earth.
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Affiliation(s)
- Ricardo Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal.,Instituto Nacional de Investigação Agrária e Veterinária, Portugal
| | - Nazua L Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
| | - Catarina M Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
| | - Claudia Andreini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
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49
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Campbell IJ, Atkinson JT, Carpenter MD, Myerscough D, Su L, Ajo-Franklin CM, Silberg JJ. Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion. Biochemistry 2022; 61:1337-1350. [PMID: 35687533 DOI: 10.1021/acs.biochem.2c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate the binding of MtrA to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). The EET efficiency was found to be inversely correlated with the proximity of the insertion to the heme prosthetic groups. Mutants with decreased EET efficiencies also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular cytochrome MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET efficiencies. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III) respiration conditions correlated with anode reduction. The peptide insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for the regulation of EET.
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Affiliation(s)
- Ian J Campbell
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Matthew D Carpenter
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Dru Myerscough
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Lin Su
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Caroline M Ajo-Franklin
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
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50
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Lewis DK, Oh Y, Mohanam LN, Wierzbicki M, Ing NL, Gu L, Hochbaum A, Wu R, Cui Q, Sharifzadeh S. Electronic Structure of de Novo Peptide ACC-Hex from First Principles. J Phys Chem B 2022; 126:4289-4298. [PMID: 35671500 DOI: 10.1021/acs.jpcb.2c02346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proteins are promising components for bioelectronic devices due in part to their biocompatibility, flexibility, and chemical diversity, which enable tuning of material properties. Indeed, an increasingly broad range of conductive protein supramolecular materials have been reported. However, due to their structural and environmental complexity, the electronic structure, and hence conductivity, of protein assemblies is not well-understood. Here we perform an all-atom simulation of the physical and electronic structure of a recently synthesized self-assembled peptide antiparallel coiled-coil hexamer, ACC-Hex. Using classical molecular dynamics and first-principles density functional theory, we examine the interactions of each peptide, containing phenylalanine residues along a hydrophobic core, to form a hexamer structure. We find that while frontier electronic orbitals are composed of phenylalanine, the peptide backbone and remaining residues, including those influenced by solvent, also contribute to the electronic density. Additionally, by studying dimers extracted from the hexamer, we show that structural distortions due to atomic fluctuations significantly impact the electronic structure of the peptide bundle. These results indicate that it is necessary to consider the full atomistic picture when using the electronic structure of supramolecular protein complexes to predict electronic properties.
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Affiliation(s)
- D Kirk Lewis
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Younghoon Oh
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Luke Nambi Mohanam
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michał Wierzbicki
- Department of Materials Science and Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Nicole L Ing
- Department of Materials Science and Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Lei Gu
- Department of Physics, University of California Irvine, Irvine, California 92697, United States
| | - Allon Hochbaum
- Department of Materials Science and Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Ruqian Wu
- Department of Physics, University of California Irvine, Irvine, California 92697, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, Boston, Massachusetts 02215, United States
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