1
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Saghaï A, Hallin S. Diversity and ecology of NrfA-dependent ammonifying microorganisms. Trends Microbiol 2024; 32:602-613. [PMID: 38462391 DOI: 10.1016/j.tim.2024.02.007] [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: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024]
Abstract
Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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2
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Li Y, Qiao S, Guo M, Zhang L, Liu G, Zhou J. Biological Self-Assembled Transmembrane Electron Conduits for High-Efficiency Ammonia Production in Microbial Electrosynthesis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7457-7468. [PMID: 38642050 DOI: 10.1021/acs.est.3c10897] [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: 04/22/2024]
Abstract
Usually, CymA is irreplaceable as the electron transport hub in Shewanella oneidensis MR-1 bidirectional electron transfer. In this work, biologically self-assembled FeS nanoparticles construct an artificial electron transfer route and implement electron transfer from extracellular into periplasmic space without CymA involvement, which present similar properties to type IV pili. Bacteria are wired up into a network, and more electron transfer conduits are activated by self-assembled transmembrane FeS nanoparticles (electron conduits), thereby substantially enhancing the ammonia production. In this study, we achieved an average NH4+-N production rate of 391.8 μg·h-1·L reactor-1 with the selectivity of 98.0% and cathode efficiency of 65.4%. Additionally, the amide group in the protein-like substances located in the outer membrane was first found to be able to transfer electrons from extracellular into intracellular with c-type cytochromes. Our work provides a new viewpoint that contributes to a better understanding of the interconnections between semiconductor materials and bacteria and inspires the exploration of new electron transfer chain components.
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Affiliation(s)
- Yao Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, P.R. China
| | - Sen Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, P.R. China
| | - Meiwei Guo
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, P.R. China
| | - Liying Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, P.R. China
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, P.R. China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian116024, P.R. China
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3
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Zang Y, Cao B, Zhao H, Xie B, Ge Y, Liu H, Yi Y. Mechanism and applications of bidirectional extracellular electron transfer of Shewanella. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:1863-1877. [PMID: 37787043 DOI: 10.1039/d3em00224a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Electrochemically active microorganisms (EAMs) play an important role in the fields of environment and energy. Shewanella is the most common EAM. Research into Shewanella contributes to a deeper comprehension of EAMs and expands practical applications. In this review, the outward and inward extracellular electron transfer (EET) mechanisms of Shewanella are summarized and the roles of riboflavin in outward and inward EET are compared. Then, four methods for the enhancement of EET performance are discussed, focusing on riboflavin, intracellular reducing force, biofilm formation and substrate spectrum, respectively. Finally, the applications of Shewanella in the environment are classified, and the restrictions are discussed. Potential solutions and promising prospects for Shewanella are also provided.
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Affiliation(s)
- Yuxuan Zang
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, No. 37, Xueyuan Road, Haidian District, Beijing 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
| | - Bo Cao
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, No. 37, Xueyuan Road, Haidian District, Beijing 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
| | - Hongyu Zhao
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, No. 37, Xueyuan Road, Haidian District, Beijing 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
| | - Beizhen Xie
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, No. 37, Xueyuan Road, Haidian District, Beijing 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
| | - Yanhong Ge
- Infore Environment Technology Group, Foshan 528000, Guangdong Province, China
| | - Hong Liu
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, No. 37, Xueyuan Road, Haidian District, Beijing 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
| | - Yue Yi
- School of Life, Beijing Institute of Technology, No. 5, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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4
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Bird LJ, Leary DH, Hervey J, Compton J, Phillips D, Tender LM, Voigt CA, Glaven SM. Marine Biofilm Engineered to Produce Current in Response to Small Molecules. ACS Synth Biol 2023; 12:1007-1020. [PMID: 36926839 DOI: 10.1021/acssynbio.2c00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Engineered electroactive bacteria have potential applications ranging from sensing to biosynthesis. In order to advance the use of engineered electroactive bacteria, it is important to demonstrate functional expression of electron transfer modules in chassis adapted to operationally relevant conditions, such as non-freshwater environments. Here, we use the Shewanella oneidensis electron transfer pathway to induce current production in a marine bacterium, Marinobacter atlanticus, during biofilm growth in artificial seawater. Genetically encoded sensors optimized for use in Escherichia coli were used to control protein expression in planktonic and biofilm attached cells. Significant current production required the addition of menaquinone, which M. atlanticus does not produce, for electron transfer from the inner membrane to the expressed electron transfer pathway. Current through the S. oneidensis pathway in M. atlanticus was observed when inducing molecules were present during biofilm formation. Electron transfer was also reversible, indicating that electron transfer into M. atlanticus could be controlled. These results show that an operationally relevant marine bacterium can be genetically engineered for environmental sensing and response using an electrical signal.
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Affiliation(s)
- Lina J Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Dagmar H Leary
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Judson Hervey
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Jaimee Compton
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Daniel Phillips
- Biochemistry Branch, Oak Ridge Institute for Science and Education/US Army DEVCOM Chemical Biological Center, Aberdeen Proving Grounds, Maryland 21005, United States
| | - Leonard M Tender
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Christopher A Voigt
- Department of Biological Engineering and the Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
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5
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Ford K, Kaste JAM, Shachar-Hill Y, TerAvest MA. Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in Shewanella oneidensis MR-1. ACS Synth Biol 2022; 11:3405-3413. [PMID: 36219726 PMCID: PMC9595118 DOI: 10.1021/acssynbio.2c00323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 01/24/2023]
Abstract
Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix carbon dioxide is one route to overcoming the limitations of photosynthetic organisms. In this work, we describe a pipeline that enabled the deletion of a conditionally essential gene from the Shewanella oneidensis MR-1 genome. S. oneidensis is a simple bacterial host that could be used for electricity-driven conversion of carbon dioxide in the future with further genetic engineering. We used Flux Balance Analysis (FBA) to model carbon and energy flows in central metabolism and assess the effects of single and double gene deletions. We modeled the growth of deletion strains under several alternative conditions to identify substrates that restore viability to an otherwise lethal gene knockout. These predictions were tested in vivo using a Mobile-CRISPRi gene knockdown system. The information learned from FBA and knockdown experiments informed our strategy for gene deletion, allowing us to successfully delete an "expected essential" gene, gpmA. FBA predicted, knockdown experiments supported, and deletion confirmed that the "essential" gene gpmA is not needed for survival, dependent on the medium used. Removal of gpmA is a first step toward driving electrode-powered CO2 fixation via RuBisCO. This work demonstrates the potential for broadening the scope of genetic engineering in S. oneidensis as a synthetic biology chassis. By combining computational analysis with a CRISPRi knockdown system in this way, one can systematically assess the impact of conditionally essential genes and use this knowledge to generate mutations previously thought unachievable.
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Affiliation(s)
- Kathryne
C. Ford
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Microbiology and Molecular Genetics, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Joshua A. M. Kaste
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yair Shachar-Hill
- Department
of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Michaela A. TerAvest
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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6
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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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7
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Jeuken LJC. Biodegradation of pollutants by exoelectrogenic bacteria is not always performed extracellularly. Environ Microbiol 2022; 24:1835-1837. [PMID: 35199430 PMCID: PMC9305215 DOI: 10.1111/1462-2920.15942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Lars J C Jeuken
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300RA, Leiden, the Netherlands
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8
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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9
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Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
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10
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Boes DM, Godoy-Hernandez A, McMillan DGG. Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life. MEMBRANES 2021; 11:346. [PMID: 34066904 PMCID: PMC8151925 DOI: 10.3390/membranes11050346] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022]
Abstract
Membrane proteins can be classified into two main categories-integral and peripheral membrane proteins-depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5'-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.
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Affiliation(s)
- Deborah M. Boes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Albert Godoy-Hernandez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Duncan G. G. McMillan
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
- School of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11 222, New Zealand
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11
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Xiao X, Ma XL, Wang LG, Long F, Li TT, Zhou XT, Liu H, Wu LJ, Yu HQ. Anaerobic reduction of high-polarity nitroaromatic compounds by electrochemically active bacteria: Roles of Mtr respiratory pathway, molecular polarity, mediator and membrane permeability. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115943. [PMID: 33158624 DOI: 10.1016/j.envpol.2020.115943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Electrochemically active bacteria (EAB) are effective for the bioreduction of nitroaromatic compounds (NACs), but the exact reduction mechanisms are unclear yet. Therefore, 3-nitrobenzenesulfonate (NBS) was used to explore the biodegradation mechanism of NACs by EAB. Results show that NBS could be anaerobically degraded by Shewanella oneidensis MR-1. The generation of aminoaromatic compounds was accompanied with the NBS reduction, indicating that NBS was biodegraded via reductive approach by S. oneidensis MR-1. The impacts of NBS concentration and cell density on the NBS reduction were evaluated. The removal of NBS depends mainly on the transmembrane electron transfer of S. oneidensis MR-1. Impairment of Mtr respiratory pathway was found to mitigate the reduction of NBS, suggesting that the anaerobic biodegradation of NBS occurred extracellularly. Knocking out cymA severely impaired the extracellular reduction ability of S. oneidensis MR-1. However, the phenotype of ΔcymA mutant could be compensated by the exogenous electron mediators, implying the trans-outer membrane diffusion of mediators into the periplasmic space. This work provides a new insight into the anaerobic reduction of aromatic contaminants by EAB.
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Affiliation(s)
- Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiao-Lin Ma
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Lu-Guang Wang
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Fei Long
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Ting-Ting Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiang-Tong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Li-Jun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Han-Qing Yu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; 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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Liu W, Chen Y, Zhou X, Liu J, Zhu J, Wang S, Liu C, Sun D. The Cyclic AMP Receptor Protein, Crp, Is Required for the Decolorization of Acid Yellow 36 in Shewanella putrefaciens CN32. Front Microbiol 2020; 11:596372. [PMID: 33362744 PMCID: PMC7755654 DOI: 10.3389/fmicb.2020.596372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/15/2020] [Indexed: 01/20/2023] Open
Abstract
Shewanella shows good application potentials in the decolorization and detoxification of azo dye wastewater. However, the molecular mechanism of decolorization is still lacking. In this study, it was found that Shewanella putrefaciens CN32 exhibited good decolorization ability to various azo dyes, and a global regulatory protein cAMP receptor protein (Crp) was identified to be required for the decolorization of acid yellow 36 (AY) by constructing a transposon mutant library. Then, the molecular mechanism of AY decolorization regulated by Crp was further investigated. RT-qPCR and electrophoretic mobility shift assay (EMSA) results showed that Crp was able to directly bind to the promoter region of the cymA gene and promote its expression. Riboflavin acting as an electron shuttle could accelerate the AY decolorization efficiency of S. putrefaciens CN32 wild-type (WT) but did not show a promoting effect to Δcrp mutant and ΔcymA mutant, further confirming that Crp promotes the decolorization through regulating electron transport chains. Moreover, the mutant with cymA overexpression could slightly enhance the AY decolorization efficiency compared with the WT strain. In addition, it was found that MtrA, MtrB, and MtrC partially contribute to the electron transfer from CymA to dye molecules, and other main electron transport chains need to be identified in future experiments. This study revealed the molecular mechanism of a global regulator Crp regulating the decolorization of azo dye, which is helpful in understanding the relationship between the decolorization and other metabolic processes in S. putrefaciens CN32.
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Affiliation(s)
- Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ying Chen
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xuge Zhou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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Wang L, Ye L, Jing C. Genetic Identification of Antimonate Respiratory Reductase in Shewanella sp. ANA-3. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14107-14113. [PMID: 33054201 DOI: 10.1021/acs.est.0c03875] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial antimonate [Sb(V)] respiratory reduction is an important process regulating Sb redox transformation in the environment. However, little is known about the microbial respiratory reductase for Sb(V). Herein, we report Sb(V)-respiring reduction by Shewanella sp. ANA-3 through an arsenate respiratory reductase encoded by arrAB. Incubation experiments showed that Shewanella sp. ANA-3 mediated Sb(V)-respiring reduction, which was dependent on the cell concentration. Both protein analysis and reverse transcriptase-polymerase chain reaction results revealed that arrAB was highly expressed in Sb(V)-respiring reduction. In vivo evidence with mutants indicated that neither ANA-3-ΔarrA nor ANA-3-ΔarrB was capable of reducing Sb(V) as efficiently as the wild type, whereas complementation by the wild-type sequences of arrA and arrB rescued the mutants' ability. Our in vitro results showed that ArrAB purified by His-Tag was able to mediate Sb(V) reduction, though with much suppressed catalytic kinetics compared with As(V) reduction. The cell-concentration-dependent reduction of Sb(V) was regulated by quorum sensing via the luxS gene. This study opens a new chapter in the mechanistic understanding of microbial Sb(V) respiratory reduction.
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Affiliation(s)
- Liying Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Li Ye
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
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A Hybrid Extracellular Electron Transfer Pathway Enhances the Survival of Vibrio natriegens. Appl Environ Microbiol 2020; 86:AEM.01253-20. [PMID: 32737131 DOI: 10.1128/aem.01253-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Vibrio natriegens is the fastest-growing microorganism discovered to date, making it a useful model for biotechnology and basic research. While it is recognized for its rapid aerobic metabolism, less is known about anaerobic adaptations in V. natriegens or how the organism survives when oxygen is limited. Here, we describe and characterize extracellular electron transfer (EET) in V. natriegens, a metabolism that requires movement of electrons across protective cellular barriers to reach the extracellular space. V. natriegens performs extracellular electron transfer under fermentative conditions with gluconate, glucosamine, and pyruvate. We characterized a pathway in V. natriegens that requires CymA, PdsA, and MtrCAB for Fe(III) citrate and Fe(III) oxide reduction, which represents a hybrid of strategies previously discovered in Shewanella and Aeromonas Expression of these V. natriegens genes functionally complemented Shewanella oneidensis mutants. Phylogenetic analysis of the inner membrane quinol dehydrogenases CymA and NapC in gammaproteobacteria suggests that CymA from Shewanella diverged from Vibrionaceae CymA and NapC. Analysis of sequenced Vibrionaceae revealed that the genetic potential to perform EET is conserved in some members of the Harveyi and Vulnificus clades but is more variable in other clades. We provide evidence that EET enhances anaerobic survival of V. natriegens, which may be the primary physiological function for EET in Vibrionaceae IMPORTANCE Bacteria from the genus Vibrio occupy a variety of marine and brackish niches with fluctuating nutrient and energy sources. When oxygen is limited, fermentation or alternative respiration pathways must be used to conserve energy. In sedimentary environments, insoluble oxide minerals (primarily iron and manganese) are able to serve as electron acceptors for anaerobic respiration by microorganisms capable of extracellular electron transfer, a metabolism that enables the use of these insoluble substrates. Here, we identify the mechanism for extracellular electron transfer in Vibrio natriegens, which uses a combination of strategies previously identified in Shewanella and Aeromonas We show that extracellular electron transfer enhanced survival of V. natriegens under fermentative conditions, which may be a generalized strategy among Vibrio spp. predicted to have this metabolism.
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Wu Y, Luo X, Qin B, Li F, Häggblom MM, Liu T. Enhanced Current Production by Exogenous Electron Mediators via Synergy of Promoting Biofilm Formation and the Electron Shuttling Process. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:7217-7225. [PMID: 32352288 DOI: 10.1021/acs.est.0c00141] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Exogenous electron mediators (EMs) can facilitate extracellular electron transfer (EET) via electron shuttling processes, but it is still unclear whether and how biofilm formation is affected by the presence of EMs. Here, the impacts of EMs on EET and biofilm formation were investigated in bioelectrochemical systems (BESs) with Shewanella oneidensis MR-1, and the results showed that the presence of five different EMs led to high density current production. All the EMs substantially promoted biofilm formation with 15-36 times higher total biofilm DNA with EMs than without EMs, and they also increased the production of extracellular polymeric substances, which was favorable for biofilm formation. The current decreased substantially after removing EMs from the medium or by replacing electrodes without biofilm, suggesting that both biofilm and EMs are required for high density current production. EET-related gene expression was upregulated with EMs, resulting in the high flux of cell electron output. A synergistic mechanism was proposed: EMs in suspension were quickly reduced by the cells and reoxidized rapidly by the electrode, resulting in a microenvironment with sufficient oxidized EMs for biofilm formation, and thus, besides the well-known electron shuttling process, the EM-induced high biofilm formation and high Mtr gene expression could jointly contribute to the EET and subsequently produce a high density current. This study provides a new insight into EM-enhanced current production via regulating the biofilm formation and EET-related gene expression.
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Affiliation(s)
- Yundang Wu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
| | - Xiaobo Luo
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Baoli Qin
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Tongxu Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
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Philipp LA, Edel M, Gescher J. Genetic engineering for enhanced productivity in bioelectrochemical systems. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:1-31. [PMID: 32446410 DOI: 10.1016/bs.aambs.2020.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A shift from petrochemical processes toward a bio-based economy is one of the most advocated developments for a sustainable future. To achieve this will require the biotechnological production of platform chemicals that can be further processed by chemical engineering. Bioelectrochemical systems (BESs) are a novel tool within the biotechnology field. In BESs, microbes serve as biocatalysts for the production of biofuels and value-added compounds, as well as for the production of electricity. Although the general feasibility of bioelectrochemical processes has been demonstrated in recent years, much research has been conducted to develop biocatalysts better suited to meet industrial demands. Initially, mainly natural exoelectrogenic organisms were investigated for their performance in BESs. Driven by possibilities of recent developments in genetic engineering and synthetic biology, the spectrum of microbial catalysts and their versatility (substrate and product range) have expanded significantly. Despite these developments, there is still a tremendous gap between currently achievable space-time yields and current densities on the one hand and the theoretical limits of BESs on the other. It will be necessary to move the performance of the biocatalysts closer to the theoretical possibilities in order to establish viable production routines. This review summarizes the status quo of engineering microbial biocatalysts for anode-applications with high space-time yields. Furthermore, we will address some of the theoretical limitations of these processes exemplarily and discuss which of the present strategies might be combined to achieve highly synergistic effects and, thus, meet industrial demands.
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Affiliation(s)
- Laura-Alina Philipp
- Karlsruhe Institute of Technology, Institute for Applied Biosciences-Department of Applied Biology, Karlsruhe, Germany
| | - Miriam Edel
- Karlsruhe Institute of Technology, Institute for Applied Biosciences-Department of Applied Biology, Karlsruhe, Germany
| | - Johannes Gescher
- Karlsruhe Institute of Technology, Institute for Applied Biosciences-Department of Applied Biology, Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute for Biological Interfaces, Eggenstein-Leopoldshafen, Germany.
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Paquete CM, Rusconi G, Silva AV, Soares R, Louro RO. A brief survey of the "cytochromome". Adv Microb Physiol 2019; 75:69-135. [PMID: 31655743 DOI: 10.1016/bs.ampbs.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.
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Zhong Y, Shi L. Genomic Analyses of the Quinol Oxidases and/or Quinone Reductases Involved in Bacterial Extracellular Electron Transfer. Front Microbiol 2018; 9:3029. [PMID: 30619124 PMCID: PMC6295460 DOI: 10.3389/fmicb.2018.03029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/23/2018] [Indexed: 11/18/2022] Open
Abstract
To exchange electrons with extracellular substrates, some microorganisms employ extracellular electron transfer (EET) pathways that physically connect extracellular redox reactions to intracellular metabolic activity. These pathways are made of redox and structural proteins that work cooperatively to transfer electrons between extracellular substrates and the cytoplasmic membrane. Crucial to the bacterial and archaeal EET pathways are the quinol oxidases and/or quinone reductases in the cytoplasmic membrane where they recycle the quinone/quinol pool in the cytoplasmic membrane during EET reaction. Up to date, three different families of quinol oxidases and/or quinone reductases involved in bacterial EET have been discovered. They are the CymA, CbcL/MtrH/MtoC, and ImcH families of quinol oxidases and/or quinone reductases that are all multiheme c-type cytochromes (c-Cyts). To investigate to what extent they are distributed among microorganisms, we search the bacterial as well as archaeal genomes for the homologs of these c-Cyts. Search results reveal that the homologs of these c-Cyts are only found in the Domain Bacteria. Moreover, the CymA homologs are only found in the phylum of Proteobacteria and most of them are in the Shewanella genus. In addition to Shewanella sp., CymA homologs are also found in other Fe(III)-reducing bacteria, such as of Vibrio parahaemolyticus. In contrast to CymA, CbcL/MtrH/MtoC, and ImcH homologs are much more widespread. CbcL/MtrH/MtoC homologs are found in 15 phyla, while ImcH homologs are found in 12 phyla. Furthermore, the heme-binding motifs of CbcL/MtrH/MtoC and ImcH homologs vary greatly, ranging from 3 to 23 and 6 to 10 heme-binding motifs for CbcL/MtrH/MtoC and ImcH homologs, respectively. Moreover, CymA and CbcL/MtrH/MtoC homologs are found in both Fe(III)-reducing and Fe(II)-oxidizing bacteria, suggesting that these families of c-Cyts catalyze both quinol-oxidizing and quinone-reducing reactions. ImcH homologs are only found in the Fe(III)-reducing bacteria, implying that they are only the quinol oxidases. Finally, some bacteria have the homologs of two different families of c-Cyts, which may improve the bacterial capability to exchange electrons with extracellular substrates.
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Affiliation(s)
- Yuhong Zhong
- Department of Biological Sciences and Technology, School of Environmental Studies, 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
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Divergent Nrf Family Proteins and MtrCAB Homologs Facilitate Extracellular Electron Transfer in Aeromonas hydrophila. Appl Environ Microbiol 2018; 84:AEM.02134-18. [PMID: 30266730 DOI: 10.1128/aem.02134-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/26/2018] [Indexed: 01/05/2023] Open
Abstract
Extracellular electron transfer (EET) is a strategy for respiration in which electrons generated from metabolism are moved outside the cell to a terminal electron acceptor, such as iron or manganese oxide. EET has primarily been studied in two model systems, Shewanella oneidensis and Geobacter sulfurreducens Metal reduction has also been reported in numerous microorganisms, including Aeromonas spp., which are ubiquitous Gammaproteobacteria found in aquatic ecosystems, with some species capable of pathogenesis in humans and fish. Genomic comparisons of Aeromonas spp. revealed a potential outer membrane conduit homologous to S. oneidensis MtrCAB. While the ability to respire metals and mineral oxides is not widespread in the genus Aeromonas, 90% of the sequenced Aeromonas hydrophila isolates contain MtrCAB homologs. A. hydrophila ATCC 7966 mutants lacking mtrA are unable to reduce metals. Expression of A. hydrophila mtrCAB in an S. oneidensis mutant lacking homologous components restored metal reduction. Although the outer membrane conduits for metal reduction were similar, homologs of the S. oneidensis inner membrane and periplasmic EET components CymA, FccA, and CctA were not found in A. hydrophila We characterized a cluster of genes predicted to encode components related to a formate-dependent nitrite reductase (NrfBCD), here named NetBCD (for Nrf-like electron transfer), and a predicted diheme periplasmic cytochrome, PdsA (periplasmic diheme shuttle). We present genetic evidence that proteins encoded by this cluster facilitate electron transfer from the cytoplasmic membrane across the periplasm to the MtrCAB conduit and function independently from an authentic NrfABCD system. A. hydrophila mutants lacking pdsA and netBCD were unable to reduce metals, while heterologous expression of these genes could restore metal reduction in an S. oneidensis mutant background. EET may therefore allow A. hydrophila and other species of Aeromonas to persist and thrive in iron- or manganese-rich oxygen-limited environments.IMPORTANCE Metal-reducing microorganisms are used for electricity production, bioremediation of toxic compounds, wastewater treatment, and production of valuable compounds. Despite numerous microorganisms being reported to reduce metals, the molecular mechanism has primarily been studied in two model systems, Shewanella oneidensis and Geobacter sulfurreducens We have characterized the mechanism of extracellular electron transfer in Aeromonas hydrophila, which uses the well-studied Shewanella system, MtrCAB, to move electrons across the outer membrane; however, most Aeromonas spp. appear to use a novel mechanism to transfer electrons from the inner membrane through the periplasm and to the outer membrane. The conserved use of MtrCAB in Shewanella spp. and Aeromonas spp. for metal reduction and conserved genomic architecture of metal reduction genes in Aeromonas spp. may serve as genomic markers for identifying metal-reducing microorganisms from genomic or transcriptomic sequencing. Understanding the variety of pathways used to reduce metals can allow for optimization and more efficient design of microorganisms used for practical applications.
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Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J. Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Mol Microbiol 2018; 109:571-583. [PMID: 29995975 DOI: 10.1111/mmi.14067] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach the cell surface and what the minimal set of electron transport proteins to the cell surface is. Nevertheless, even after decades of work in different research groups around the globe there are still several important questions that were not answered yet. In particular, the physiology of this organism, the possible evolutionary benefit of some responses to anoxic conditions, as well as the exact mechanism of electron transfer onto solid electron acceptors are yet to be addressed. The elucidation of these questions will be a great challenge for future work and important for the application of extracellular respiration in biotechnological processes.
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Affiliation(s)
- Sebastian Beblawy
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Thea Bursac
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Catarina Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Ricardo Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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Hsu L, Deng P, Zhang Y, Jiang X. Core/Shell Bacterial Cables: A One-Dimensional Platform for Probing Microbial Electron Transfer. NANO LETTERS 2018; 18:4606-4610. [PMID: 29923733 DOI: 10.1021/acs.nanolett.8b01908] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Extracellular electron transfer (EET) from electrochemically active bacteria (EAB) plays a critical role in renewable bioelectricity harvesting through microbial fuel cells (MFC). Comprehensive interpretation and interrogation of EET mechanisms can provide valuable information to enhance MFC performance, which however are still restricted by the intrinsic complexity of natural biofilm. Here, we design core/shell EAB-encapsulating cables as a one-dimensional model system to facilitate EET studies, where the local microenvironments can be rationally controlled to establish structure-function correlations with full biological relevance. In particular, our proof-of-concept studies with Shewanella loihica PV-4 ( S. loihica) encapsulating cables demonstrate the precise modulation of fiber diameters (from 6.9 ± 1.1 to 25.1 ± 2.4 μm) and bacteria interactions, which are found to play important roles in programming the formation of different intercellular structures as revealed by in situ optical and ex situ electron microscopic studies. As-formed bacterial cables exhibit conductivity in the range of 2.5-16.2 mS·cm-1, which is highly dependent on the bacteria density as well as the nature and number of intercellular interconnections. Under electron-acceptor limited conditions, the closely contacted bacteria promote the development of high density self-assembling nanomaterials at cellular interfaces which can be directly translated to the increase of EET efficiency (16.2 mS·cm-1) as compared with isolated, remotely connected bacteria samples (6.4 mS·cm-1). Introducing exceeding concentrations of soluble electron acceptors during cell culture, however, substantially suppresses the formation of cellular interconnections and leads to significantly reduced conductivity (2.5 mS·cm-1). Frequency-dependent measurements further reveal that EET of EAB networks share similar characteristics to electron hopping in conductive polymer matrix, including dominant direct current-conduction in the low frequency region, and alternating current-induced additional electron hopping when the applied frequency is above the critical frequency (105 Hz). The current work represents a strategically new approach for noninvasively probing EET with rationally defined microenvironment and cellular interactions across a wide range of length scales, which is expected to open up new opportunities for tackling the fundamentals and implications of EET.
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Affiliation(s)
- Leo Hsu
- Department of Biomedical Engineering , Tufts University , Medford , Massachusetts 02155 , United States
| | - Pu Deng
- Department of Biomedical Engineering , Tufts University , Medford , Massachusetts 02155 , United States
| | - Yixin Zhang
- Department of Biomedical Engineering , Tufts University , Medford , Massachusetts 02155 , United States
| | - Xiaocheng Jiang
- Department of Biomedical Engineering , Tufts University , Medford , Massachusetts 02155 , United States
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De la Cruz Barrón M, Merlin C, Guilloteau H, Montargès-Pelletier E, Bellanger X. Suspended Materials in River Waters Differentially Enrich Class 1 Integron- and IncP-1 Plasmid-Carrying Bacteria in Sediments. Front Microbiol 2018; 9:1443. [PMID: 30013540 PMCID: PMC6036612 DOI: 10.3389/fmicb.2018.01443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aquatic ecosystems are frequently considered as the final receiving environments of anthropogenic pollutants such as pharmaceutical residues or antibiotic resistant bacteria, and as a consequence tend to form reservoirs of antibiotic resistance genes. Considering the global threat posed by the antibiotic resistance, the mechanisms involved in both the formation of such reservoirs and their remobilization are a concern of prime importance. Antibiotic resistance genes are strongly associated with mobile genetic elements that are directly involved in their dissemination. Most mobile genetic element-mediated gene transfers involve replicative mechanisms and, as such, localized gene transfers should participate in the local increase in resistance gene abundance. Additionally, the carriage of conjugative mobile elements encoding cell appendages acting as adhesins has already been demonstrated to increase biofilm-forming capability of bacteria and, therefore, should also contribute to their selective enrichment on surfaces. In the present study, we investigated the occurrence of two families of mobile genetic elements, IncP-1 plasmids and class 1 integrons, in the water column and bank sediments of the Orne River, in France. We show that these mobile elements, especially IncP-1 plasmids, are enriched in the bacteria attached on the suspended matters in the river waters, and that a similar abundance is found in freshly deposited sediments. Using the IncP-1 plasmid pB10 as a model, in vitro experiments demonstrated that local enrichment of plasmid-bearing bacteria on artificial surfaces mainly resulted from an increase in bacterial adhesion properties conferred by the plasmid rather than an improved dissemination frequency of the plasmid between surface-attached bacteria. We propose plasmid-mediated adhesion to particles to be one of the main contributors in the formation of mobile genetic element-reservoirs in sediments, with adhesion to suspended matter working as a selective enrichment process of antibiotic resistant genes and bacteria.
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Dissociation between Iron and Heme Biosyntheses Is Largely Accountable for Respiration Defects of Shewanella oneidensis fur Mutants. Appl Environ Microbiol 2018; 84:AEM.00039-18. [PMID: 29427425 DOI: 10.1128/aem.00039-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/30/2018] [Indexed: 11/20/2022] Open
Abstract
Iron, a major protein cofactor, is essential for most organisms but can simultaneously be toxic. Iron homeostasis thus has to be effectively maintained under a range of iron regimes. This may be particularly true with Shewanella oneidensis, a representative of dissimilatory metal-reducing bacteria (DMRB), which are capable of respiring a variety of chemicals as electron acceptors (EAs), including iron ores. Although iron respiration and its regulation have been extensively studied in this bacterium, how iron homeostasis is maintained remains largely unknown. Here, we report that the loss of the iron homeostasis master regulator Fur negatively affects the respiration of all EAs tested. This defect appears mainly to be a result of reduced cytochrome c (cyt c) production, despite a decrease in the expression of reductases that are under the direct control of Fur. We also show that S. oneidensis Fur interacts with canonical Fur box motifs in F-F-x-R configuration rather than the palindromic motif proposed before. The fur mutant has lowered total iron and increased free iron contents. Under iron-rich conditions, overproduction of the major iron storage protein Bfr elevates the total iron levels of the fur mutant over those of the wild-type but does not affect free iron levels. Intriguingly, such an operation only marginally improves cyt c production by affecting heme b biosynthesis. It is established that iron dictates heme b/cyt c biosynthesis in S. oneidensis fur + strains, but the fur mutation annuls the dependence of heme b/cyt c biosynthesis on iron. Overall, our results suggest that Fur has a profound impact on the iron homeostasis of S. oneidensis, through which many physiological processes, especially respiration, are transformed.IMPORTANCE Iron reduction is a signature of S. oneidensis, and this process relies on a large number of type c cytochromes, which per se are iron-containing proteins. Thus, iron plays an essential and special role in iron respiration, but to date, the nature of iron metabolism and regulation of the bacterium remains largely unknown. In this study, we investigated impacts of Fur, the master regulator of iron homeostasis, on respiration. The loss of Fur causes a general defect in respiration, a result of impaired cyt c production rather than specific regulation. Additionally, the fur mutant is unresponsive to iron, resulting in imbalanced iron homeostasis and dissociation between iron and cyt c production. These findings provide important insights into the iron biology of DMRB.
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Hirose A, Kasai T, Aoki M, Umemura T, Watanabe K, Kouzuma A. Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways. Nat Commun 2018; 9:1083. [PMID: 29540717 PMCID: PMC5852097 DOI: 10.1038/s41467-018-03416-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/09/2018] [Indexed: 01/08/2023] Open
Abstract
Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. We also show that an Arc regulatory system is involved in sensing electrode potentials and regulating the expression of catabolic genes, including those for NADH dehydrogenase. We suggest that these findings may facilitate the use of EAB in biotechnological processes and offer the molecular bases for their ecological strategies in natural habitats.
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Affiliation(s)
- Atsumi Hirose
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Takuya Kasai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Motohide Aoki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tomonari Umemura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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Xiao X, Li TT, Lu XR, Feng XL, Han X, Li WW, Li Q, Yu HQ. A simple method for assaying anaerobic biodegradation of dyes. BIORESOURCE TECHNOLOGY 2018; 251:204-209. [PMID: 29277051 DOI: 10.1016/j.biortech.2017.12.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic dye degradation is usually assayed using serum vials, which is time-consuming and costly. In this work, a simple method was established for real-time nondestructive assay of dye biodegradation using 96-well microtiter plates with petrolatum oil to avoid the volatilization and high transmittance transparent tape to prevent the permeation of oxygen. With the anaerobic degradation of methyl red and amaranth by Shewanella oneidensis MR-1, this assay method was verified. Further experiments revealed that blocking Mtr pathway had no substantial effect on the degradation of methyl red and dose of riboflavin also failed to promote the degradation of methyl red. On the contrary, the anaerobic degradation of amaranth depended mainly on the electron transmembrane transfer through Mtr pathway. Our work clearly indicates that Mtr pathway had different effects on intra- and extra-cellular degradation of azo dyes by S. oneidensis MR-1. Such a developed method is helpful for investigating anaerobic dye decolorization.
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Affiliation(s)
- Xiang Xiao
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Ting-Ting Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xue-Rong Lu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiao-Li Feng
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xue Han
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Qian Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China.
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Meibom KL, Cabello EM, Bernier-Latmani R. The Small RNA RyhB Is a Regulator of Cytochrome Expression in Shewanella oneidensis. Front Microbiol 2018. [PMID: 29515549 PMCID: PMC5826389 DOI: 10.3389/fmicb.2018.00268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Shewanella oneidensis produces an extensive electron transfer network that results in metabolic flexibility. A large number of c-type cytochromes are expressed by S. oneidensis and these function as the fundamental electron transport chain proteins. Although several S. oneidensis cytochromes have been well-characterized, little is known about how their expression is regulated. In this study, we investigate the role of the ferric uptake regulator (Fur) and the sRNA RyhB in regulation. Our results demonstrate that loss of Fur leads to diminished growth and an apparent decrease in heme-containing proteins. Remarkably, deleting the Fur-repressed ryhB gene almost completely reverses these physiological changes, indicating that the phenotypes resulting from loss of Fur are (at least partially) dependent on RyhB. RNA sequencing identified a number of possible RyhB repressed genes. A large fraction of these encode c-type cytochromes, among them two of the most abundant periplasmic cytochromes CctA (also known as STC) and ScyA. We show that RyhB destabilizes the mRNA of four of its target genes, cctA, scyA, omp35, and nrfA and this requires the presence of the RNA chaperone Hfq. Iron limitation decreases the expression of the RyhB target genes cctA and scyA and this regulation relies on the presence of both Fur and RyhB. Overall, this study suggests that controlling cytochrome expression is of importance to maintain iron homeostasis and that sRNAs molecules are important players in the regulation of fundamental processes in S. oneidensis MR-1.
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Affiliation(s)
- Karin L Meibom
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elena M Cabello
- Bioinformatics and Biostatistics Core Facility, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Effect of the anode potential on the physiology and proteome of Shewanella oneidensis MR-1. Bioelectrochemistry 2018; 119:172-179. [DOI: 10.1016/j.bioelechem.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 11/19/2022]
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Harris HW, Sánchez-Andrea I, McLean JS, Salas EC, Tran W, El-Naggar MY, Nealson KH. Redox Sensing within the Genus Shewanella. Front Microbiol 2018; 8:2568. [PMID: 29422884 PMCID: PMC5789149 DOI: 10.3389/fmicb.2017.02568] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/11/2017] [Indexed: 11/28/2022] Open
Abstract
A novel bacterial behavior called congregation was recently described in Shewanella oneidensis MR-1 as the accumulation of cells around insoluble electron acceptors (IEA). It is the result of a series of "run-and-reversal" events enabled by modulation of swimming speed and direction. The model proposed that the swimming cells constantly sense their surroundings with specialized outer membrane cytochromes capable of extracellular electron transport (EET). Up to this point, neither the congregation nor attachment behavior have been studied in any other strains. In this study, the wild type of S. oneidensis MR-1 and several deletion mutants as well as eight other Shewanella strains (Shewanella putrefaciens CN32, S. sp. ANA-3, S. sp. W3-18-1, Shewanella amazonensis SB2B, Shewanella loihica PV-4, Shewanella denitrificans OS217, Shewanella baltica OS155, and Shewanella frigidimarina NCIMB400) were screened for the ability to congregate. To monitor congregation and attachment, specialized cell-tracking techniques, as well as a novel cell accumulation after photo-bleaching (CAAP) confocal microscopy technique were utilized in this study. We found a strong correlation between the ability of strain MR-1 to accumulate on mineral surface and the presence of key EET genes such as mtrBC/omcA (SO_1778, SO_1776, and SO_1779) and gene coding for methyl-accepting protein (MCPs) with Ca+ channel chemotaxis receptor (Cache) domain (SO_2240). These EET and taxis genes were previously identified as essential for characteristic run and reversal swimming around IEA surfaces. CN32, ANA-3, and PV-4 congregated around both Fe(OH)3 and MnO2. Two other Shewanella spp. showed preferences for one oxide over the other: preferences that correlated with the metal content of the environments from which the strains were isolated: e.g., W3-18-1, which was isolated from an iron-rich habitat congregated and attached preferentially to Fe(OH)3, while SB2B, which was isolated from a MnO2-rich environment, preferred MnO2.
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Affiliation(s)
- Howard W. Harris
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | | | - Jeffrey S. McLean
- Department of Periodontics, University of Washington, Seattle, WA, United States
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States
| | | | - William Tran
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | - Mohamed Y. El-Naggar
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
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Han R, Li X, Wu Y, Li F, Liu T. In situ spectral kinetics of quinone reduction by c-type cytochromes in intact Shewanella oneidensis MR-1 cells. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2017.02.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Loss of OxyR reduces efficacy of oxygen respiration in Shewanella oneidensis. Sci Rep 2017; 7:42609. [PMID: 28195212 PMCID: PMC5307378 DOI: 10.1038/srep42609] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/11/2017] [Indexed: 02/02/2023] Open
Abstract
In many bacteria, OxyR is the major regulator controlling cellular response to H2O2. A common phenotype resulting from OxyR loss is reduced growth rate, but the underlying mechanism is unknown. We demonstrated in Shewanella oneidensis, an important research model for applied and environmental microbes, that the defect is primarily due to an electron shortage to major terminal oxidase cytochrome cbb3. The loss of OxyR leads to enhanced production of electron carriers that compete for electrons against cytochrome cbb3, cytochrome bd in particular. We further showed that the oxyR mutation also results in increased production of menaquinone, an additional means to lessen electrons to cytochrome cbb3. Although regulation of OxyR on these biological processes appears to be indirect, these data indicate that the regulator plays a previously underappreciated role in mediating respiration.
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Cherkouk A, Law GTW, Rizoulis A, Law K, Renshaw JC, Morris K, Livens FR, Lloyd JR. Influence of riboflavin on the reduction of radionuclides by Shewanella oneidenis MR-1. Dalton Trans 2016; 45:5030-7. [PMID: 26632613 DOI: 10.1039/c4dt02929a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uranium (as UO2(2+)), technetium (as TcO4(-)) and neptunium (as NpO2(+)) are highly mobile radionuclides that can be reduced enzymatically by a range of anaerobic and facultatively anaerobic microorganisms, including Shewanella oneidensis MR-1, to poorly soluble species. The redox chemistry of Pu is more complicated, but the dominant oxidation state in most environments is highly insoluble Pu(IV), which can be reduced to Pu(III) which has a potentially increased solubility which could enhance migration of Pu in the environment. Recently it was shown that flavins (riboflavin and flavin mononucleotide (FMN)) secreted by Shewanella oneidensis MR-1 can act as electron shuttles, promoting anoxic growth coupled to the accelerated reduction of poorly-crystalline Fe(III) oxides. Here, we studied the role of riboflavin in mediating the reduction of radionuclides in cultures of Shewanella oneidensis MR-1. Our results demonstrate that the addition of 10 μM riboflavin enhances the reduction rate of Tc(VII) to Tc(IV), Pu(IV) to Pu(III) and to a lesser extent, Np(V) to Np(IV), but has no significant influence on the reduction rate of U(VI) by Shewanella oneidensis MR-1. Thus riboflavin can act as an extracellular electron shuttle to enhance rates of Tc(VII), Np(V) and Pu(IV) reduction, and may therefore play a role in controlling the oxidation state of key redox active actinides and fission products in natural and engineered environments. These results also suggest that the addition of riboflavin could be used to accelerate the bioremediation of radionuclide-contaminated environments.
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Affiliation(s)
- Andrea Cherkouk
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK.
| | - Gareth T W Law
- Centre for Radiochemistry Research, School of Chemistry, Manchester, M13 9PL, UK
| | - Athanasios Rizoulis
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK.
| | - Katie Law
- Centre for Radiochemistry Research, School of Chemistry, Manchester, M13 9PL, UK
| | - Joanna C Renshaw
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK.
| | - Katherine Morris
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK.
| | - Francis R Livens
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK. and Centre for Radiochemistry Research, School of Chemistry, Manchester, M13 9PL, UK
| | - Jonathan R Lloyd
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK.
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Liu DF, Min D, Cheng L, Zhang F, Li DB, Xiao X, Sheng GP, Yu HQ. Anaerobic reduction of 2,6-dinitrotoluene by Shewanella oneidensis
MR-1: Roles of Mtr respiratory pathway and NfnB. Biotechnol Bioeng 2016; 114:761-768. [DOI: 10.1002/bit.26212] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/22/2016] [Accepted: 10/31/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
| | - Lei Cheng
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
| | - Feng Zhang
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
| | - Dao-Bo Li
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
| | - Xiang Xiao
- School of Environment and Safety Engineering; Jiangsu University; Zhenjiang 212013 China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion; University of Science and Technology of China; Hefei 230026 China
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NapB in excess inhibits growth of Shewanella oneidensis by dissipating electrons of the quinol pool. Sci Rep 2016; 6:37456. [PMID: 27857202 PMCID: PMC5114592 DOI: 10.1038/srep37456] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023] Open
Abstract
Shewanella, a group of ubiquitous bacteria renowned for respiratory versatility, thrive in environments where various electron acceptors (EAs) of different chemical and physiological characteristics coexist. Despite being extensively studied, we still know surprisingly little about strategies by which multiple EAs and their interaction define ecophysiology of these bacteria. Previously, we showed that nitrite inhibits growth of the genus representative Shewanella oneidensis on fumarate and presumably some other CymA (quinol dehydrogenase)-dependent EAs by reducing cAMP production, which in turn leads to lowered expression of nitrite and fumarate reductases. In this study, we demonstrated that inhibition of fumarate growth by nitrite is also attributable to overproduction of NapB, the cytochrome c subunit of nitrate reductase. Further investigations revealed that excessive NapB per se inhibits growth on all EAs tested, including oxygen. When overproduced, NapB acts as an electron shuttle to dissipate electrons of the quinol pool, likely to extracellullar EAs, because the Mtr system, the major electron transport pathway for extracellular electron transport, is implicated. The study not only sheds light on mechanisms by which certain EAs, especially toxic ones, impact the bacterial ecophysiology, but also provides new insights into how electron shuttle c-type cytochromes regulate multi-branched respiratory networks.
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Jin M, Fu H, Yin J, Yuan J, Gao H. Molecular Underpinnings of Nitrite Effect on CymA-Dependent Respiration in Shewanella oneidensis. Front Microbiol 2016; 7:1154. [PMID: 27493647 PMCID: PMC4954811 DOI: 10.3389/fmicb.2016.01154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022] Open
Abstract
Shewanella exhibit a remarkable versatility of respiration, with a diverse array of electron acceptors (EAs). In environments where these bacteria thrive, multiple EAs are usually present. However, we know little about strategies by which these EAs and their interaction affect ecophysiology of Shewanella. In this study, we demonstrate in the model strain, Shewanella oneidensis MR-1, that nitrite, not through nitric oxide to which it may convert, inhibits respiration of fumarate, and probably many other EAs whose reduction depends on quinol dehydrogenase CymA. This is achieved via the repression of cyclic adenosine monophosphate (cAMP) production, a second messenger required for activation of cAMP-receptor protein (Crp) which plays a primary role in regulation of respiration. If nitrite is not promptly removed, intracellular cAMP levels drop, and this impairs Crp activity. As a result, the production of nitrite reductase NrfA, CymA, and fumarate reductase FccA is substantially reduced. In contrast, nitrite can be simultaneously respired with trimethylamine N-oxide, resulting in enhanced biomass.
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Affiliation(s)
- Miao Jin
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Huihui Fu
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Jianhua Yin
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Jie Yuan
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
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Han R, Li F, Liu T, Li X, Wu Y, Wang Y, Chen D. Effects of Incubation Conditions on Cr(VI) Reduction by c-type Cytochromes in Intact Shewanella oneidensis MR-1 Cells. Front Microbiol 2016; 7:746. [PMID: 27242759 PMCID: PMC4872037 DOI: 10.3389/fmicb.2016.00746] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/03/2016] [Indexed: 11/13/2022] Open
Abstract
It is widely recognized that the outer membrane c-type cytochromes (OM c-Cyts) of metal-reducing bacteria play a key role in microbial metal reduction processes. However, the in situ redox status of OM c-Cyts during microbial metal reduction processes remain poorly understood. In this study, diffuse-transmission UV/Vis spectroscopy is used to investigate the in situ spectral reaction of Cr(VI) reduction by c-Cyts in intact Shewanella oneidensis MR-1 cells under different incubation conditions. The reduced c-Cyts decreased transiently at the beginning and then recovered gradually over time. The Cr(VI) reduction rates decreased with increasing initial Cr(VI) concentrations, and Cr(III) was identified as a reduced product. The presence of Cr(III) substantially inhibited Cr(VI) reduction and the recovery of reduced c-Cyts, indicating that Cr(III) might inhibit cell growth. Cr(VI) reduction rates increased with increasing cell density. The highest Cr(VI) reduction rate and fastest recovery of c-Cyts were obtained at pH 7.0 and 30°C, with sodium lactate serving as an electron donor. The presence of O2 strongly inhibited Cr(VI) reduction, suggesting that O2 might compete with Cr(VI) as an electron acceptor in cells. This study provides a case of directly examining in vivo reaction properties of an outer-membrane enzyme during microbial metal reduction processes under non-invasive physiological conditions.
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Affiliation(s)
- Rui Han
- School of Environment and Energy, South China University of TechnologyGuangzhou, China; Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil SciencesGuangzhou, China
| | - Fangbai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences Guangzhou, China
| | - Tongxu Liu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences Guangzhou, China
| | - Xiaomin Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences Guangzhou, China
| | - Yundang Wu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences Guangzhou, China
| | - Ying Wang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences Guangzhou, China
| | - Dandan Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences Guangzhou, China
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Choi AR, Kim MS, Kang SG, Lee HS. Dimethyl sulfoxide reduction by a hyperhermophilic archaeon Thermococcus onnurineus NA1 via a cysteine-cystine redox shuttle. J Microbiol 2016; 54:31-38. [DOI: 10.1007/s12275-016-5574-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
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Breuer M, Rosso KM, Blumberger J, Butt JN. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. J R Soc Interface 2015; 12:20141117. [PMID: 25411412 DOI: 10.1098/rsif.2014.1117] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
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Affiliation(s)
- Marian Breuer
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Julea N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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38
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Alves MN, Neto SE, Alves AS, Fonseca BM, Carrêlo A, Pacheco I, Paquete CM, Soares CM, Louro RO. Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1. Front Microbiol 2015; 6:665. [PMID: 26175726 PMCID: PMC4484225 DOI: 10.3389/fmicb.2015.00665] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/17/2015] [Indexed: 01/14/2023] Open
Abstract
The versatile anaerobic metabolism of the Gram-negative bacterium Shewanella oneidensis MR-1 (SOMR-1) relies on a multitude of redox proteins found in its periplasm. Most are multiheme cytochromes that carry electrons to terminal reductases of insoluble electron acceptors located at the cell surface, or bona fide terminal reductases of soluble electron acceptors. In this study, the interaction network of several multiheme cytochromes was explored by a combination of NMR spectroscopy, activity assays followed by UV-visible spectroscopy and comparison of surface electrostatic potentials. From these data the small tetraheme cytochrome (STC) emerges as the main periplasmic redox shuttle in SOMR-1. It accepts electrons from CymA and distributes them to a number of terminal oxidoreductases involved in the respiration of various compounds. STC is also involved in the electron transfer pathway to reduce nitrite by interaction with the octaheme tetrathionate reductase (OTR), but not with cytochrome c nitrite reductase (ccNiR). In the main pathway leading the metal respiration STC pairs with flavocytochrome c (FccA), the other major periplasmic cytochrome, which provides redundancy in this important pathway. The data reveals that the two proteins compete for the binding site at the surface of MtrA, the decaheme cytochrome inserted on the periplasmic side of the MtrCAB-OmcA outer-membrane complex. However, this is not observed for the MtrA homologues. Indeed, neither STC nor FccA interact with MtrD, the best replacement for MtrA, and only STC is able to interact with the decaheme cytochrome DmsE of the outer-membrane complex DmsEFABGH. Overall, these results shown that STC plays a central role in the anaerobic respiratory metabolism of SOMR-1. Nonetheless, the trans-periplasmic electron transfer chain is functionally resilient as a consequence of redundancies that arise from the presence of alternative pathways that bypass/compete with STC.
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Affiliation(s)
- Mónica N Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Sónia E Neto
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Alexandra S Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Bruno M Fonseca
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Afonso Carrêlo
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Isabel Pacheco
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Catarina M Paquete
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cláudio M Soares
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo O Louro
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
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39
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Kouzuma A, Kasai T, Hirose A, Watanabe K. Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells. Front Microbiol 2015; 6:609. [PMID: 26136738 PMCID: PMC4468914 DOI: 10.3389/fmicb.2015.00609] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/02/2015] [Indexed: 12/12/2022] Open
Abstract
Shewanella oneidensis MR-1 is a facultative anaerobe that respires using a variety of inorganic and organic compounds. MR-1 is also capable of utilizing extracellular solid materials, including anodes in microbial fuel cells (MFCs), as electron acceptors, thereby enabling electricity generation. As MFCs have the potential to generate electricity from biomass waste and wastewater, MR-1 has been extensively studied to identify the molecular systems that are involved in electricity generation in MFCs. These studies have demonstrated the importance of extracellular electron-transfer (EET) pathways that electrically connect the quinone pool in the cytoplasmic membrane to extracellular electron acceptors. Electricity generation is also dependent on intracellular catabolic pathways that oxidize electron donors, such as lactate, and regulatory systems that control the expression of genes encoding the components of catabolic and electron-transfer pathways. In addition, recent findings suggest that cell-surface polymers, e.g., exopolysaccharides, and secreted chemicals, which function as electron shuttles, are also involved in electricity generation. Despite these advances in our knowledge on the EET processes in MR-1, further efforts are necessary to fully understand the underlying intra- and extracellular molecular systems for electricity generation in MFCs. We suggest that investigating how MR-1 coordinates these systems to efficiently transfer electrons to electrodes and conserve electrochemical energy for cell proliferation is important for establishing the biological basis for MFCs.
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Takuya Kasai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Atsumi Hirose
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
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40
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Sturm-Richter K, Golitsch F, Sturm G, Kipf E, Dittrich A, Beblawy S, Kerzenmacher S, Gescher J. Unbalanced fermentation of glycerol in Escherichia coli via heterologous production of an electron transport chain and electrode interaction in microbial electrochemical cells. BIORESOURCE TECHNOLOGY 2015; 186:89-96. [PMID: 25812811 DOI: 10.1016/j.biortech.2015.02.116] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 05/28/2023]
Abstract
Microbial electrochemical cells are an emerging technology for achieving unbalanced fermentations. However, organisms that can serve as potential biocatalysts for this application are limited by their narrow substrate spectrum. This study describes the reprogramming of Escherichia coli for the efficient use of anodes as electron acceptors. Electron transfer into the periplasm was accelerated by 183% via heterologous expression of the c-type cytochromes CymA, MtrA and STC from Shewanella oneidensis. STC was identified as a target for heterologous expression via a two-stage screening approach. First, mass spectroscopic analysis revealed natively expressed cytochromes in S. oneidensis. Thereafter, the corresponding genes were cloned and expressed in E. coli to quantify periplasmic electron transfer activity using methylene blue. This redox dye was further used to expand electron transfer to carbon electrode surfaces. The results demonstrate that E. coli can be reprogrammed from glycerol fermentation to respiration upon production of the new electron transport chain.
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Affiliation(s)
- Katrin Sturm-Richter
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Frederik Golitsch
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Gunnar Sturm
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Elena Kipf
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany
| | - André Dittrich
- Institute of Photogrammetry and Remote Sensing, Englerstraße 7, D-76131 Karlsruhe, Germany
| | - Sebastian Beblawy
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sven Kerzenmacher
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany
| | - Johannes Gescher
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany.
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41
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Tikhonova TV, Popov VO. Structural and functional studies of multiheme cytochromes c involved in extracellular electron transport in bacterial dissimilatory metal reduction. BIOCHEMISTRY (MOSCOW) 2015; 79:1584-601. [DOI: 10.1134/s0006297914130094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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43
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Electroactive bacteria—molecular mechanisms and genetic tools. Appl Microbiol Biotechnol 2014; 98:8481-95. [DOI: 10.1007/s00253-014-6005-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
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44
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Fu H, Jin M, Ju L, Mao Y, Gao H. Evidence for function overlapping of CymA and the cytochrome bc1 complex in the Shewanella oneidensis nitrate and nitrite respiration. Environ Microbiol 2014; 16:3181-95. [PMID: 24650148 DOI: 10.1111/1462-2920.12457] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/23/2014] [Accepted: 03/16/2014] [Indexed: 11/29/2022]
Abstract
Shewanella oneidensis is an important model organism for its versatility of anaerobic respiration. CymA, a cytoplasmic membrane-bound tetraheme c-type cytochrome, plays a central role in anaerobic respiration by transferring electrons from the quinone pool to a variety of terminal reductases. Although loss of CymA results in defect in respiration of many electron acceptors (EAs), a significant share of the capacity remains in general. In this study, we adopted a transposon random mutagenesis method in a cymA null mutant to identify substituent(s) of CymA with respect to nitrite and nitrate respiration. A total of 87 insertion mutants, whose ability to reduce nitrite was further impaired, were obtained. Among the interrupted genes, the petABC operon appeared to be the most likely candidate given the involvement of the cytochrome bc1 complex that it encodes in electron transport. Subsequent analyses not only confirmed that the complex and CymA were indeed functionally overlapping in nitrate/nitrite respiration but also revealed that both proteins were able to draw electrons from ubiquinone and menaquinone. Furthermore, we found that expression of the bc1 complex was affected by oxygen but not nitrate or nitrite and by global regulators ArcA and Crp in an indirect manner.
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Affiliation(s)
- Huihui Fu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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45
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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46
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Fuller SJ, McMillan DGG, Renz MB, Schmidt M, Burke IT, Stewart DI. Extracellular electron transport-mediated Fe(III) reduction by a community of alkaliphilic bacteria that use flavins as electron shuttles. Appl Environ Microbiol 2014; 80:128-37. [PMID: 24141133 PMCID: PMC3910996 DOI: 10.1128/aem.02282-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/09/2013] [Indexed: 11/20/2022] Open
Abstract
The biochemical and molecular mechanisms used by alkaliphilic bacterial communities to reduce metals in the environment are currently unknown. We demonstrate that an alkaliphilic (pH > 9) consortium dominated by Tissierella, Clostridium, and Alkaliphilus spp. is capable of using iron (Fe(3+)) as a final electron acceptor under anaerobic conditions. Iron reduction is associated with the production of a freely diffusible species that, upon rudimentary purification and subsequent spectroscopic, high-performance liquid chromatography, and electrochemical analysis, has been identified as a flavin species displaying properties indistinguishable from those of riboflavin. Due to the link between iron reduction and the onset of flavin production, it is likely that riboflavin has an import role in extracellular metal reduction by this alkaliphilic community.
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Affiliation(s)
- Samuel J. Fuller
- School of Civil Engineering, University of Leeds, Leeds, United Kingdom
| | | | - Marc B. Renz
- University Hospital Jena, Friedrich-Schiller University, Jena, Germany
| | - Martin Schmidt
- University Hospital Jena, Friedrich-Schiller University, Jena, Germany
| | - Ian T. Burke
- School of Earth and Environment, University of Leeds, Leeds, United Kingdom
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47
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Jin M, Jiang Y, Sun L, Yin J, Fu H, Wu G, Gao H. Unique organizational and functional features of the cytochrome c maturation system in Shewanella oneidensis. PLoS One 2013; 8:e75610. [PMID: 24040415 PMCID: PMC3769277 DOI: 10.1371/journal.pone.0075610] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/16/2013] [Indexed: 11/19/2022] Open
Abstract
Shewanella are renowned for their ability to respire on a wide range of electron acceptors, which has been partially accredited to the presence of a large number of the c-type cytochromes. In the model species S. oneidensis MR-1, at least 41 genes encode c-type cytochromes that are predicted to be intact, thereby likely functional. Previously, in-frame deletion mutants for 36 of these genes were obtained and characterized. In this study, first we completed the construction of an entire set of c-type cytochrome mutants utilizing a newly developed att-based mutagenesis approach, which is more effective and efficient than the approach used previously by circumventing the conventional cloning. Second, we investigated the cytochrome c maturation (Ccm) system in S. oneidensis. There are two loci predicted to encode components of the Ccm system, SO0259-SO0269 and SO0476-SO0478. The former is proven essential for cytochrome c maturation whereas the latter is dispensable. Unlike the single operon organization observed in other γ-proteobacteria, genes at the SO0259-SO0269 locus are uniquely organized into four operons, ccmABCDE, scyA, SO0265, and ccmFGH-SO0269. Functional analysis revealed that the SO0265 gene rather than the scyA and SO0269 genes are relevant to cytochrome c maturation.
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Affiliation(s)
- Miao Jin
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yaoming Jiang
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Linlin Sun
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianhua Yin
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huihui Fu
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Genfu Wu
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haichun Gao
- College of Life Sciences and Institute of Microbiology, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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48
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McMillan DGG, Marritt SJ, Firer-Sherwood MA, Shi L, Richardson DJ, Evans SD, Elliott SJ, Butt JN, Jeuken LJC. Protein-protein interaction regulates the direction of catalysis and electron transfer in a redox enzyme complex. J Am Chem Soc 2013; 135:10550-6. [PMID: 23799249 PMCID: PMC3823026 DOI: 10.1021/ja405072z] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Protein–protein interactions
are well-known to regulate
enzyme activity in cell signaling and metabolism. Here, we show that
protein–protein interactions regulate the activity of a respiratory-chain
enzyme, CymA, by changing the direction or bias of catalysis. CymA,
a member of the widespread NapC/NirT superfamily, is a menaquinol-7
(MQ-7) dehydrogenase that donates electrons to several distinct terminal
reductases in the versatile respiratory network of Shewanella oneidensis. We report the incorporation
of CymA within solid-supported membranes that mimic the inner membrane
architecture of S. oneidensis. Quartz-crystal
microbalance with dissipation (QCM-D) resolved the formation of a
stable complex between CymA and one of its native redox partners,
flavocytochrome c3 (Fcc3) fumarate reductase.
Cyclic voltammetry revealed that CymA alone could only reduce MQ-7,
while the CymA-Fcc3 complex catalyzed the reaction required
to support anaerobic respiration, the oxidation of MQ-7. We propose
that MQ-7 oxidation in CymA is limited by electron transfer to the
hemes and that complex formation with Fcc3 facilitates
the electron-transfer rate along the heme redox chain. These results
reveal a yet unexplored mechanism by which bacteria can regulate multibranched
respiratory networks through protein–protein interactions.
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Affiliation(s)
- Duncan G G McMillan
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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49
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Mind the gap: diversity and reactivity relationships among multihaem cytochromes of the MtrA/DmsE family. Biochem Soc Trans 2013; 40:1268-73. [PMID: 23176466 DOI: 10.1042/bst20120106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Shewanella oneidensis MR-1 has the ability to use many external terminal electron acceptors during anaerobic respiration, such as DMSO. The pathway that facilitates this electron transfer includes the decahaem cytochrome DmsE, a paralogue of the MtrA family of decahaem cytochromes. Although both DmsE and MtrA are decahaem cytochromes implicated in the long-range electron transfer across a ~300 Å (1 Å=0.1 nm) wide periplasmic 'gap', MtrA has been shown to be only 105 Å in maximal length. In the present paper, DmsE is further characterized via protein film voltammetry, revealing that the electrochemistry of the DmsE haem cofactors display macroscopic potentials lower than those of MtrA by 100 mV. It is possible this tuning of the redox potential of DmsE is required to shuttle electrons to the outer-membrane proteins specific to DMSO reduction. Other decahaem cytochromes found in S. oneidensis, such as the outer-membrane proteins MtrC, MtrF and OmcA, have been shown to have electrochemical properties similar to those of MtrA, yet possess a different evolutionary relationship.
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50
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The roles of CymA in support of the respiratory flexibility of Shewanella oneidensis MR-1. Biochem Soc Trans 2013; 40:1217-21. [PMID: 23176457 DOI: 10.1042/bst20120150] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Shewanella species are isolated from the oxic/anoxic regions of seawater and aquatic sediments where redox conditions fluctuate in time and space. Colonization of these environments is by virtue of flexible respiratory chains, many of which are notable for the ability to reduce extracellular substrates including the Fe(III) and Mn(IV) contained in oxide and phyllosilicate minerals. Shewanella oneidensis MR-1 serves as a model organism to consider the biochemical basis of this flexibility. In the present paper, we summarize the various systems that serve to branch the respiratory chain of S. oneidensis MR-1 in order that electrons from quinol oxidation can be delivered the various terminal electron acceptors able to support aerobic and anaerobic growth. This serves to highlight several unanswered questions relating to the regulation of respiratory electron transport in Shewanella and the central role(s) of the tetrahaem-containing quinol dehydrogenase CymA in that process.
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