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Xia J, Li Y, Jiang X, Chen D, Shen J. Enhanced 4-bromophenol anaerobic biodegradation in electricity-stimulated anaerobic system: The key role of humic acid in reshaping microbial eco-interrelations and functions. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131426. [PMID: 37084513 DOI: 10.1016/j.jhazmat.2023.131426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
Electricity-stimulated anaerobic system (ESAS) has shown great potential for halogenated organic pollutants removal. Exogenous redox mediators can improve electron transfer efficiency to enhance pollutants removal in ESAS. In this study, humic acid (HA), a low-cost electron mediator, was added into ESAS to enhance the simultaneous reductive debromination and mineralization of 4-bromophenol (4-BP). Results showed that the highest 4-BP removal efficiency at 48 h was 95.43 % with HA dosage of 30 mg/L at - 700 mV, which was 34.67 % higher than that without HA. The addition of HA decreased the requirement for electron donors and enriched Petrimonas and Rhodococcus for humus respiratory. HA addition regulated microbial interactions, and enhanced species cooperation between Petrimonas and dehalogenation species (Thauera and Desulfovibrio), phenol degradation-related species (Rhodococcus) as well as fermentative species (Desulfobulbus). Functional genes related to 4-BP degradation (dhaA/hemE/xylC/chnB/dmpN) and electron transfer (etfB/nuoA/qor/ccoN/coxA) were increased in abundance by HA addition. The enhanced microbial functions, as well as species cooperation and facilitation, all contributed to the improved 4-BP biodegradation in HA-added ESAS. This study provided a deep insight into microbial mechanism driven by HA and offered a promising strategy for improving halogenated organic pollutants removal from wastewater.
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Affiliation(s)
- Jiaohui Xia
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yan Li
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xinbai Jiang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Dan Chen
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jinyou Shen
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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2
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You Z, Li J, Wang Y, Wu D, Li F, Song H. Advances in mechanisms and engineering of electroactive biofilms. Biotechnol Adv 2023; 66:108170. [PMID: 37148984 DOI: 10.1016/j.biotechadv.2023.108170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/22/2023] [Accepted: 05/02/2023] [Indexed: 05/08/2023]
Abstract
Electroactive biofilms (EABs) are electroactive microorganisms (EAMs) encased in conductive polymers that are secreted by EAMs and formed by the accumulation and cross-linking of extracellular polysaccharides, proteins, nucleic acids, lipids, and other components. EABs are present in the form of multicellular aggregates and play a crucial role in bioelectrochemical systems (BESs) for diverse applications, including biosensors, microbial fuel cells for renewable bioelectricity production and remediation of wastewaters, and microbial electrosynthesis of valuable chemicals. However, naturally occurred EABs are severely limited owing to their low electrical conductivity that seriously restrict the electron transfer efficiency and practical applications. In the recent decade, synthetic biology strategies have been adopted to elucidate the regulatory mechanisms of EABs, and to enhance the formation and electrical conductivity of EABs. Based on the formation of EABs and extracellular electron transfer (EET) mechanisms, the synthetic biology-based engineering strategies of EABs are summarized and reviewed as follows: (i) Engineering the structural components of EABs, including strengthening the synthesis and secretion of structural elements such as polysaccharides, eDNA, and structural proteins, to improve the formation of biofilms; (ii) Enhancing the electron transfer efficiency of EAMs, including optimizing the distribution of c-type cytochromes and conducting nanowire assembly to promote contact-based EET, and enhancing electron shuttles' biosynthesis and secretion to promote shuttle-mediated EET; (iii) Incorporating intracellular signaling molecules in EAMs, including quorum sensing systems, secondary messenger systems, and global regulatory systems, to increase the electron transfer flux in EABs. This review lays a foundation for the design and construction of EABs for diverse BES applications.
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Affiliation(s)
- Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianxun Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yuxuan Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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3
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Wang XM, Wang L, Chen L, Tian LJ, Zhu TT, Wu QZ, Hu YR, Zheng LR, Li WW. AQDS Activates Extracellular Synergistic Biodetoxification of Copper and Selenite via Altering the Coordination Environment of Outer-Membrane Proteins. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13786-13797. [PMID: 36098667 DOI: 10.1021/acs.est.2c04130] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The biotransformation of heavy metals in the environment is usually affected by co-existing pollutants like selenium (Se), which may lower the ecotoxicity of heavy metals, but the underlying mechanisms remain unclear. Here, we shed light on the pathways of copper (Cu2+) and selenite (SeO32-) synergistic biodetoxification by Shewanella oneidensis MR-1 and illustrate how such processes are affected by anthraquinone-2,6-disulfonate (AQDS), an analogue of humic substances. We observed the formation of copper selenide nanoparticles (Cu2-xSe) from synergistic detoxification of Cu2+ and SeO32- in the periplasm. Interestingly, adding AQDS triggered a fundamental transition from periplasmic to extracellular reaction, enabling 14.7-fold faster Cu2+ biodetoxification (via mediated electron transfer) and 11.4-fold faster SeO32- detoxification (via direct electron transfer). This is mainly attributed to the slightly raised redox potential of the heme center of AQDS-coordinated outer-membrane proteins that accelerates electron efflux from the cells. Our work offers a fundamental understanding of the synergistic detoxification of heavy metals and Se in a complicated environmental matrix and unveils an unexpected role of AQDS beyond electron mediation, which may guide the development of more efficient environmental remediation and resource recovery biotechnologies.
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Affiliation(s)
- Xue-Meng Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
- USTC-CityU Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou 215123, China
| | - Li Wang
- School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei 230026, China
| | - Lin Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
- USTC-CityU Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou 215123, China
| | - Li-Jiao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, China
| | - Ting-Ting Zhu
- School of Public Health, Anhui Medical University, Hefei 230032, China
| | - Qi-Zhong Wu
- USTC-CityU Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou 215123, China
- School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei 230026, China
| | - Yi-Rong Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
- USTC-CityU Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou 215123, China
| | - Li-Rong Zheng
- Beijing Synchrotron Radiation Laboratory, Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
- USTC-CityU Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou 215123, China
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4
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Perry EK, Meirelles LA, Newman DK. From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance. Nat Rev Microbiol 2022; 20:129-142. [PMID: 34531577 PMCID: PMC8857043 DOI: 10.1038/s41579-021-00620-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Secondary metabolites profoundly affect microbial physiology, metabolism and stress responses. Increasing evidence suggests that these molecules can modulate microbial susceptibility to commonly used antibiotics; however, secondary metabolites are typically excluded from standard antimicrobial susceptibility assays. This may in part account for why infections by diverse opportunistic bacteria that produce secondary metabolites often exhibit discrepancies between clinical antimicrobial susceptibility testing results and clinical treatment outcomes. In this Review, we explore which types of secondary metabolite alter antimicrobial susceptibility, as well as how and why this phenomenon occurs. We discuss examples of molecules that opportunistic and enteric pathogens either generate themselves or are exposed to from their neighbours, and the nuanced impacts these molecules can have on tolerance and resistance to certain antibiotics.
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Affiliation(s)
- Elena K Perry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lucas A Meirelles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
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5
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Zhu TT, Cheng ZH, Yu SS, Li WW, Liu DF, Yu HQ. Unexpected role of electron-transfer hub in direct degradation of pollutants by exoelectrogenic bacteria. Environ Microbiol 2022; 24:1838-1848. [PMID: 35170205 DOI: 10.1111/1462-2920.15939] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 01/28/2022] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Exoelectrogenic bacteria (EEB) are capable of anaerobic respiration with diverse extracellular electron acceptors including insoluble minerals, electrodes and flavins, but the detailed electron transfer pathways and reaction mechanisms remain elusive. Here, we discover that CymA, which is usually considered to solely serve as an inner-membrane electron transfer hub in Shewanella oneidensis MR-1 (a model EEB), might also function as a reductase for direct reducing diverse nitroaromatic compounds (e.g., 2,4-dichloronitrobenzene) and azo dyes. Such a process can be accelerated by dosing anthraquinone-2,6-disulfonate. The CymA-based reduction pathways in S. oneidensis MR-1 for different contaminants could be functionally reconstructed and strengthened in Escherichia coli. The direct reduction of lowly polar contaminants by quinol oxidases like CymA homologs might be universal in diverse microbes. This work offers new insights into the pollutant reduction mechanisms of EEB and unveils a new function of CymA to act as a terminal reductase. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ting-Ting Zhu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhou-Hua Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Sheng-Song Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,University of Science and Technology of China-City University of Hong Kong Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou, 215123, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,Anhui Key Laboratory of Sewage Purification and Ecological Rehabilitation Materials, Hefei, 230601, China
| | - Han-Qing Yu
- 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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6
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Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea. THE ISME JOURNAL 2022; 16:168-177. [PMID: 34285362 PMCID: PMC8692474 DOI: 10.1038/s41396-021-01047-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.
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7
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Hirose N, Kazama I, Sato R, Tanaka T, Aso Y, Ohara H. Microbial fuel cells using α-amylase-displaying Escherichia coli with starch as fuel. J Biosci Bioeng 2021; 132:519-523. [PMID: 34454829 DOI: 10.1016/j.jbiosc.2021.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/18/2022]
Abstract
Escherichia coli JM109 (pGV3-SBA) can assimilate starch by fusing the starch-digesting enzyme α-amylase from Streptococcus bovis NRIC1535 to an OprI' lipoprotein anchor on the cell membrane. This study shows microbial fuel cells (MFCs) development using this recombinant type of E. coli and starch as fuel. We observed the current generation of MFCs with E. coli JM109 (pGV3-SBA) for 120 h. During this period, it consumed 7.1 g/L of starch. A mediator in the form of anthraquinone-2,6-disulfonic acid disodium salt at 0.2, 0.4, and 0.8 mM was added to the MFCs. The highest maximum-current density (271 mA/m2) and maximum-power density (29.3 mW/m2) performances occurred in the 0.4 mM mediator solution. Coulomb yields were calculated as 3.4%, 3.0%, and 3.5% in 1.0, 5.0, and 10.0 g/L of initial starch, respectively. The concentrations of acetic acid, succinic acid, fumaric acid, and ethanol as metabolites were determined. In particular, 38.3 mM of ethanol was produced from 7.1 g/L of starch. This study suggests the use of recombinant E. coli which can assimilate starch present in starch-fueled MFCs. Moreover, it proposes the possibility of gene recombination technology for using wide variety of biomass as fuel and improving MFC's performance.
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Affiliation(s)
- Naoto Hirose
- Department of Biobased Materials Science, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Iori Kazama
- Department of Biobased Materials Science, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Rintaro Sato
- Department of Biobased Materials Science, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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8
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Rowe AR, Salimijazi F, Trutschel L, Sackett J, Adesina O, Anzai I, Kugelmass LH, Baym MH, Barstow B. Identification of a pathway for electron uptake in Shewanella oneidensis. Commun Biol 2021; 4:957. [PMID: 34381156 PMCID: PMC8357807 DOI: 10.1038/s42003-021-02454-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO2 and renewable electricity1-6. Theoretically EET could do this with an efficiency comparable to H2-oxidation7,8 but without the need for a volatile intermediate and the problems it causes for scale up9. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-110-14, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation15.
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Affiliation(s)
- Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Leah Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Joshua Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | | | - Isao Anzai
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Liat H Kugelmass
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Michael H Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
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9
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Metal Reduction and Protein Secretion Genes Required for Iodate Reduction by Shewanella oneidensis. Appl Environ Microbiol 2019; 85:AEM.02115-18. [PMID: 30446562 DOI: 10.1128/aem.02115-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 01/28/2023] Open
Abstract
The metal-reducing gammaproteobacterium Shewanella oneidensis reduces iodate (IO3 -) as an anaerobic terminal electron acceptor. Microbial IO3 - electron transport pathways are postulated to terminate with nitrate (NO3 -) reductase, which reduces IO3 - as an alternative electron acceptor. Recent studies with S. oneidensis, however, have demonstrated that NO3 - reductase is not involved in IO3 - reduction. The main objective of the present study was to determine the metal reduction and protein secretion genes required for IO3 - reduction by Shewanella oneidensis with lactate, formate, or H2 as the electron donor. With all electron donors, the type I and type V protein secretion mutants retained wild-type IO3 - reduction activity, while the type II protein secretion mutant lacking the outer membrane secretin GspD was impaired in IO3 - reduction. Deletion mutants lacking the cyclic AMP receptor protein (CRP), cytochrome maturation permease CcmB, and inner membrane-tethered c-type cytochrome CymA were impaired in IO3 - reduction with all electron donors, while deletion mutants lacking c-type cytochrome MtrA and outer membrane β-barrel protein MtrB of the outer membrane MtrAB module were impaired in IO3 - reduction with only lactate as an electron donor. With all electron donors, mutants lacking the c-type cytochromes OmcA and MtrC of the metal-reducing extracellular electron conduit MtrCAB retained wild-type IO3 - reduction activity. These findings indicate that IO3 - reduction by S. oneidensis involves electron donor-dependent metal reduction and protein secretion pathway components, including the outer membrane MtrAB module and type II protein secretion of an unidentified IO3 - reductase to the S. oneidensis outer membrane.IMPORTANCE Microbial iodate (IO3 -) reduction is a major component in the biogeochemical cycling of iodine and the bioremediation of iodine-contaminated environments; however, the molecular mechanism of microbial IO3 - reduction is poorly understood. Results of the present study indicate that outer membrane (type II) protein secretion and metal reduction genes encoding the outer membrane MtrAB module of the extracellular electron conduit MtrCAB are required for IO3 - reduction by S. oneidensis On the other hand, the metal-reducing c-type cytochrome MtrC of the extracellular electron conduit is not required for IO3 - reduction by S. oneidensis These findings indicate that the IO3 - electron transport pathway terminates with an as yet unidentified IO3 - reductase that associates with the outer membrane MtrAB module to deliver electrons extracellularly to IO3.
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10
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Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes. mSphere 2019; 4:4/1/e00436-18. [PMID: 30674644 PMCID: PMC6344600 DOI: 10.1128/msphere.00436-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog. Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog. These genes were particularly rich in the bog’s anoxic hypolimnion and were found in diverse bacterial lineages, some of which are relatives of known iron oxidizers or iron-HS reducers. We hypothesize that HS may be a previously overlooked electron acceptor and that EET-enabled redox cycling may be important in pelagic respiration and greenhouse gas budget in humic-rich freshwater lakes.
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11
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Zhou C, Wang H, Si Y, Wu K, Yousaf A. Electron shuttles enhance the degradation of sulfamethoxazole coupled with Fe(III) reduction by Shewanella oneidensis MR-1. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 62:156-163. [PMID: 30029095 DOI: 10.1016/j.etap.2018.07.006] [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: 02/22/2018] [Revised: 06/19/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The ability of anthraquinone-2,6-disulfonate (AQDS) and riboflavin to enhance the sulfamethoxazole (SMX) degradation coupled with the Fe(III) reduction by Shewanella oneidensis MR-1 was investigated. The results indicated that the SMX degradation rate was 38.5% with an initial SMX concentration at 0.04 mM. For the overall performance of AQDS and riboflavin mediated SMX degradation and iron reduction, the SMX degradation rate was gradually increased with the enhancement of iron reduction. Riboflavin had a stronger enhancement on SMX degradation and iron reduction than AQDS, but the enhancement was not positively correlated with electron shuttles concentration. A quantitative characterization of the electron transfer capacity (ETC) of the electron shuttles showed that the ETC was higher for riboflavin than AQDS. The S. oneidensis MR-1 16S rRNA gene copies results indicated that electron shuttles had a positive effect on the microbial activity of S. oneidensis MR-1. The LCMS result indicated that the products of the SMX biodegradation were 3-amino-5-methylisoxazole and 4-aminobenzenesulfonic acid, which suggested that the SMX biodegradation was caused by SN bond cleavage. This study indicates that the biochemical mechanisms play a vital role in SMX transformation and Fe(II) generation in this system.
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Affiliation(s)
- Chen Zhou
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Huiqing Wang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Youbin Si
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Kang Wu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Amina Yousaf
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
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12
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Martinez CM, Alvarez LH. Application of redox mediators in bioelectrochemical systems. Biotechnol Adv 2018; 36:1412-1423. [DOI: 10.1016/j.biotechadv.2018.05.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/15/2018] [Accepted: 05/26/2018] [Indexed: 12/12/2022]
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13
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Microbial electrocatalysis: Redox mediators responsible for extracellular electron transfer. Biotechnol Adv 2018; 36:1815-1827. [PMID: 30196813 DOI: 10.1016/j.biotechadv.2018.07.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 11/21/2022]
Abstract
Redox mediator plays an important role in extracellular electron transfer (EET) in many environments wherein microbial electrocatalysis occurs actively. Because of the block of cell envelope and the low difference of redox potential between the intracellular and extracellular surroundings, the proceeding of EET depends mainly on the help of a variety of mediators that function as an electron carrier or bridge. In this Review, we will summarize a wide range of redox mediators and further discuss their functional mechanisms in EET that drives a series of microbial electrocatalytic reactions. Studying these mediators adds to our knowledge of how charge transport and electrochemical reactions occur at the microorganism-electrode interface. This understanding would promote the widespread applications of microbial electrocatalysis in microbial fuel cells, bioremediation, bioelectrosynthesis, biomining, nanomaterial productions, etc. These improved applications will greatly benefit the sustainable development of the environmental-friendly biochemical industries.
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14
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Dantas JM, Ferreira MR, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analogue for humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:619-630. [PMID: 29777686 DOI: 10.1016/j.bbabio.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/09/2018] [Accepted: 05/15/2018] [Indexed: 01/17/2023]
Abstract
The bacterium Geobacter sulfurreducens can transfer electrons to quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH2QDS) can also be used as energy source by G. sulfurreducens. Such bidirectional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bifunctional behavior toward the humic substance analogue. It can reduce AQDS but the protein can also be reduced by AH2QDS. Using stopped-flow kinetic measurements we were able to demonstrate that other periplasmic members of the PpcA-family in G. sulfurreducens (PpcB, PpcD and PpcE) also showed the same behavior. The extent of the electron transfer is thermodynamically controlled favoring the reduction of the cytochromes. NMR spectra recorded for 13C,15N-enriched samples in the presence increasing amounts of AQDS showed perturbations in the chemical shift signals of the cytochromes. The chemical shift perturbations on cytochromes backbone NH and 1H heme methyl signals were used to map their interaction regions with AQDS, showing that each protein forms a low-affinity binding complex through well-defined positive surface regions in the vicinity of heme IV (PpcB, PpcD and PpcE) and I (PpcE). Docking calculations performed using NMR chemical shift perturbations allowed modeling the interactions between AQDS and each cytochrome at a molecular level. Overall, the results obtained provided important structural-functional relationships to rationalize the microbial respiration of humic substances in G. sulfurreducens.
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Affiliation(s)
- Joana M Dantas
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Marisa R Ferreira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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15
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Michelson K, Sanford RA, Valocchi AJ, Werth CJ. Nanowires of Geobacter sulfurreducens Require Redox Cofactors to Reduce Metals in Pore Spaces Too Small for Cell Passage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11660-11668. [PMID: 28929755 DOI: 10.1021/acs.est.7b02531] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Members of the Geobacteraceae family are ubiquitous metal reducers that utilize conductive "nanowires" to reduce Mn(IV) and Fe(III) oxides in anaerobic sediments. However, it is not currently known if and to what extent the Mn(IV) and Fe(III) oxides in soil grains and low permeability sediments that are sequestered in pore spaces too small for cell passage can be reduced by long-range extracellular electron transport via Geobacter nanowires, and what mechanisms control this reduction. We developed a microfluidic reactor that physically separates Geobacter sulfurreducens from the Mn(IV) mineral birnessite by a 1.4 μm thick wall containing <200 nm pores. Using optical microscopy and Raman spectroscopy, we show that birnessite can be reduced up to 15 μm away from cell bodies, similar to the reported length of Geobacter nanowires. Reduction across the nanoporous wall required reducing conditions, provided by Escherichia coli, and an exogenous supply of riboflavin. Our results discount electron shuttling by dissolved flavins, and instead support their role as bound redox cofactors in electron transport from nanowires to metal oxides. We also show that upon addition of a soluble electron shuttle (i.e., AQDS), reduction extends beyond the reported nanowire length up to 40 μm into a layer of birnessite.
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Affiliation(s)
- Kyle Michelson
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign , 1301 West Green Street, Urbana, Illinois 61801, United States
| | - Albert J Valocchi
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Charles J Werth
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
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16
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He S, Stevens SLR, Chan LK, Bertilsson S, Glavina del Rio T, Tringe SG, Malmstrom RR, McMahon KD. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere 2017; 2:e00277-17. [PMID: 28959738 PMCID: PMC5615132 DOI: 10.1128/msphere.00277-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/05/2017] [Indexed: 11/20/2022] Open
Abstract
Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called "Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.
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Affiliation(s)
- Shaomei He
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Geoscience, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Sarah L. R. Stevens
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
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17
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Matsusako T, Toya Y, Yoshikawa K, Shimizu H. Identification of alcohol stress tolerance genes of Synechocystis sp. PCC 6803 using adaptive laboratory evolution. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:307. [PMID: 29270221 PMCID: PMC5738210 DOI: 10.1186/s13068-017-0996-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Synechocystis sp. PCC 6803 is an attractive organism for the production of alcohols, such as isobutanol and ethanol. However, because stress against the produced alcohol is a major barrier for industrial applications, it is highly desirable to engineer organisms with strong alcohol tolerance. RESULTS Isobutanol-tolerant strains of Synechocystis sp. PCC 6803 were obtained by long-term passage culture experiments using medium containing 2 g/L isobutanol. These evolved strains grew on medium containing 5 g/L isobutanol on which the parental strain could not grow. Mutation analysis of the evolved strains revealed that they acquired resistance ability due to combinatorial malfunctions of slr1044 (mcpA) and slr0369 (envD), or slr0322 (hik43) and envD. The tolerant strains demonstrated stress resistance against isobutanol as well as a wide variety of alcohols such as ethanol, n-butanol, and isopentanol. As a result of introducing an ethanol-producing pathway into the evolved strain, its productivity successfully increased to 142% of the control strain. CONCLUSIONS Novel mutations were identified that improved the stress tolerance ability of various alcohols in Synechocystis sp. PCC 6803.
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Affiliation(s)
- Takuya Matsusako
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871 Japan
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18
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Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku. Nat Commun 2016; 7:13270. [PMID: 27830751 PMCID: PMC5109470 DOI: 10.1038/ncomms13270] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/14/2016] [Indexed: 02/07/2023] Open
Abstract
Whole-genome knockout collections are invaluable for connecting gene sequence to function, yet traditionally, their construction has required an extraordinary technical effort. Here we report a method for the construction and purification of a curated whole-genome collection of single-gene transposon disruption mutants termed Knockout Sudoku. Using simple combinatorial pooling, a highly oversampled collection of mutants is condensed into a next-generation sequencing library in a single day, a 30- to 100-fold improvement over prior methods. The identities of the mutants in the collection are then solved by a probabilistic algorithm that uses internal self-consistency within the sequencing data set, followed by rapid algorithmically guided condensation to a minimal representative set of mutants, validation, and curation. Starting from a progenitor collection of 39,918 mutants, we compile a quality-controlled knockout collection of the electroactive microbe Shewanella oneidensis MR-1 containing representatives for 3,667 genes that is functionally validated by high-throughput kinetic measurements of quinone reduction. Knockout collections provide a valuable tool to explore gene function, yet are expensive and technically challenging to produce at a genome-wide scale. Here Baym et al. devise a cost-effective transposon-based method to quickly develop a knockout collection for the electroactive microbe Shewanella oneidensis.
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19
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Fowler GJS, Pereira-Medrano AG, Jaffe S, Pasternak G, Pham TK, Ledezma P, Hall STE, Ieropoulos IA, Wright PC. An iTRAQ characterisation of the role of TolC during electron transfer from Shewanella oneidensis MR-1. Proteomics 2016; 16:2764-2775. [PMID: 27599463 DOI: 10.1002/pmic.201500538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 07/20/2016] [Accepted: 09/02/2016] [Indexed: 02/04/2023]
Abstract
Anodophilic bacteria have the ability to generate electricity in microbial fuel cells (MFCs) by extracellular electron transfer to the anode. We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive Gammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture. The regulated dataset produced was enriched in membrane proteins. Proteins shown to be more abundant in anaerobic electroactive anodic cells included efflux pump TolC and an uncharacterised tetratricopeptide repeat (TPR) protein, whilst the TonB2 system and associated uncharacterised proteins such as TtpC2 and DUF3450 were more abundant in microaerobic planktonic cells. In order to validate the iTRAQ data, the functional role for TolC was examined using a δTolC knockout mutant of S. oneidensis. Possible roles for the uncharacterised proteins were identified using comparative bioinformatics. We demonstrate that employing an insoluble extracellular electron acceptor requires multiple proteins involved in cell surface properties. All MS and processed data are available via ProteomeXchange with identifier PXD004090.
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Affiliation(s)
- Gregory J S Fowler
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Ana G Pereira-Medrano
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Stephen Jaffe
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Grzegorz Pasternak
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Trong Khoa Pham
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Pablo Ledezma
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Simon T E Hall
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Ioannis A Ieropoulos
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Phillip C Wright
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK. .,Faculty of Science, Agriculture & Engineering, Newcastle University, Devonshire Building, Newcastle upon Tyne, UK.
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20
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Takeuchi Y, Khawdas W, Aso Y, Ohara H. Microbial fuel cells using Cellulomonas spp. with cellulose as fuel. J Biosci Bioeng 2016; 123:358-363. [PMID: 27818074 DOI: 10.1016/j.jbiosc.2016.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/13/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
Cellulomonas fimi, Cellulomonas biazotea, and Cellulomonas flavigena are cellulose-degrading microorganisms chosen to compare the degradation of cellulose. C. fimi degraded 2.5 g/L of cellulose within 4 days, which was the highest quantity among the three microorganisms. The electric current generation by the microbial fuel cell (MFC) using the cellulose-containing medium with C. fimi was measured over 7 days. The medium in the MFC was sampled every 24 h to quantify the degradation of cellulose, and the results showed that the electric current increased with the degradation of cellulose. The maximum electric power generated by the MFC was 38.7 mW/m2, and this numeric value was 63% of the electric power generated by an MFC with Shewanella oneidensis MR-1, a well-known current-generating microorganism. Our results showed that C. fimi was an excellent candidate to produce the electric current from cellulose via MFCs.
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Affiliation(s)
- Yuya Takeuchi
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Wichean Khawdas
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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21
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Xia ZC, Cheng YY, Kong WQ, Shi XY, Yang T, Wang MY, Huang F, Wu C. Electron shuttles alter selenite reduction pathway and redistribute formed Se(0) nanoparticles. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.12.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Wang X, Xu G, Wan C, Ren Y, Tian E. Improved biomass production by humic analog anthraquinone-2-sulfonate from kitchen waste in a two-phase system. RSC Adv 2016. [DOI: 10.1039/c5ra18240a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The volatile fatty acids from kitchen waste were used as substrates of anoxygenic photosynthetic bacteria (APB) in a dark-photo fermentation reactor, and anthraquinone-2-sulfonate (AQS) was firstly applied to boost the biomass yield.
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Affiliation(s)
- Xingzu Wang
- Key Laboratory of Reservoir Aquatic Environment
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Guihua Xu
- Key Laboratory of Reservoir Aquatic Environment
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Chunli Wan
- Key Laboratory of Reservoir Aquatic Environment
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Yiwei Ren
- Key Laboratory of Reservoir Aquatic Environment
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Enling Tian
- Key Laboratory of Reservoir Aquatic Environment
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
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23
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Szeinbaum N, Burns JL, DiChristina TJ. Electron transport and protein secretion pathways involved in Mn(III) reduction by Shewanella oneidensis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:490-500. [PMID: 25646542 DOI: 10.1111/1758-2229.12173] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Soluble Mn(III) represents an important yet overlooked oxidant in marine and freshwater systems. The molecular mechanism of microbial Mn(III) reduction, however, has yet to be elucidated. Extracellular reduction of insoluble Mn(IV) and Fe(III) oxides by the metal-reducing γ-proteobacterium Shewanella oneidensis involves inner (CymA) and outer (OmcA) membrane-associated c-type cytochromes, the extracellular electron conduit MtrCAB, and GspD, the secretin of type II protein secretion. CymA, MtrCAB and GspD mutants were unable to reduce Mn(III) and Mn(IV) with lactate, H2, or formate as electron donor. The OmcA mutant reduced Mn(III) and Mn(IV) at near wild-type rates with lactate and formate as electron donor. With H2 as electron donor, however, the OmcA mutant was unable to reduce Mn(III) but reduced Mn(IV) at wild-type rates. Analogous Fe(III) reduction rate analyses indicated that other electron carriers compensated for the absence of OmcA, CymA, MtrCAB and GspD during Fe(III) reduction in an electron donor-dependent fashion. Results of the present study demonstrate that the S. oneidensis electron transport and protein secretion components involved in extracellular electron transfer to external Mn(IV) and Fe(III) oxides are also required for electron transfer to Mn(III) and that OmcA may function as a dedicated component of an H2 oxidation-linked Mn(III) reduction system.
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24
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Dantas JM, Morgado L, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Evidence for interaction between the triheme cytochrome PpcA from Geobacter sulfurreducens and anthrahydroquinone-2,6-disulfonate, an analog of the redox active components of humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:750-60. [PMID: 24530867 DOI: 10.1016/j.bbabio.2014.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 11/25/2022]
Abstract
The bacterium Geobacter sulfurreducens displays an extraordinary respiratory versatility underpinning the diversity of electron donors and acceptors that can be used to sustain anaerobic growth. Remarkably, G. sulfurreducens can also use as electron donors the reduced forms of some acceptors, such as the humic substance analog anthraquinone-2,6-disulfonate (AQDS), a feature that confers environmentally competitive advantages to the organism. Using UV-visible and stopped-flow kinetic measurements we demonstrate that there is electron exchange between the triheme cytochrome PpcA from Gs and AQDS. 2D-(1)H-(15)N HSQC NMR spectra were recorded for (15)N-enriched PpcA samples, in the absence and presence of AQDS. Chemical shift perturbation measurements, at increasing concentration of AQDS, were used to probe the interaction region and to measure the binding affinity of the PpcA-AQDS complex. The perturbations on the NMR signals corresponding to the PpcA backbone NH and heme substituents showed that the region around heme IV interacts with AQDS through the formation of a complex with a definite life time in the NMR time scale. The comparison of the NMR data obtained for PpcA in the presence and absence of AQDS showed that the interaction is reversible. Overall, this study provides for the first time a clear illustration of the formation of an electron transfer complex between AQDS and a G. sulfurreducens triheme cytochrome, shedding light on the electron transfer pathways underlying the microbial oxidation of humics.
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Affiliation(s)
- Joana M Dantas
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Carlos A Salgueiro
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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25
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Global transcriptome analysis of Escherichia coli exposed to immobilized anthraquinone-2-sulfonate and azo dye under anaerobic conditions. Appl Microbiol Biotechnol 2013; 97:6895-905. [PMID: 23820558 DOI: 10.1007/s00253-013-5066-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/04/2013] [Accepted: 06/16/2013] [Indexed: 10/26/2022]
Abstract
The immobilization of quinone compounds is regarded as a promising strategy to accelerate anaerobic decolorization of xenobiotic compounds azo dyes in the presence of quinone-reducing microorganisms. However, little is known about the basic response of these microorganisms to immobilized quinones in the presence of azo dyes. In the present study, whole-genome DNA microarrays were used to investigate a quinone-reducing bacterium Escherichia coli K-12 transcription response to immobilized anthraquinone-2-sulfonate (AQSim) reduction and azo dye acid red 18 (AR 18) decolorization. Transcriptome analysis showed that AQSim was more accessible for the cells of E. coli K-12 than AR 18. Despite there being some differences between AQSim and soluble AQS mediated decolorization of AR 18, AQSim reduction and AR 18 decolorization, more similarity could be observed in the four processes. Among over 60 % shared genes, several groups of genes exhibited high expression levels, including those genes encoding terminal reductases, menaquinone biosynthesis, formate dehydrogenases and outer membrane proteins. Especially, nrfABCD, frdBCD and dsmABC encoding terminal reductases were significantly upregulated. Further gene deletion experiments demonstrated that the above three groups of genes were involved in AQSim-mediated AR 18 decolorization. In addition, significant upregulation of stress response genes was observed, which indicated the adaptation of E. coli K-12 to AQSim and AR 18 exposures.
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Extracellular electron transfer to Fe(III) oxides by the hyperthermophilic archaeon Geoglobus ahangari via a direct contact mechanism. Appl Environ Microbiol 2013; 79:4694-700. [PMID: 23728807 DOI: 10.1128/aem.01566-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbial reduction of Fe(III) plays an important role in the geochemistry of hydrothermal systems, yet it is poorly understood at the mechanistic level. Here we show that the obligate Fe(III)-reducing archaeon Geoglobus ahangari uses a direct-contact mechanism for the reduction of Fe(III) oxides to magnetite at 85°C. Alleviating the need to directly contact the mineral with the addition of a chelator or the electron shuttle anthraquinone-2,6-disulfonate (AQDS) stimulated Fe(III) reduction. In contrast, entrapment of the oxides within alginate beads to prevent cell contact with the electron acceptor prevented Fe(III) reduction and cell growth unless AQDS was provided. Furthermore, filtered culture supernatant fluids had no effect on Fe(III) reduction, ruling out the secretion of an endogenous mediator too large to permeate the alginate beads. Consistent with a direct contact mechanism, electron micrographs showed cells in intimate association with the Fe(III) mineral particles, which once dissolved revealed abundant curled appendages. The cells also produced several heme-containing proteins. Some of them were detected among proteins sheared from the cell's outer surface and were required for the reduction of insoluble Fe(III) oxides but not for the reduction of the soluble electron acceptor Fe(III) citrate. The results thus support a mechanism in which the cells directly attach and transfer electrons to the Fe(III) oxides using redox-active proteins exposed on the cell surface. This strategy confers on G. ahangari a competitive advantage for accessing and reducing Fe(III) oxides under the extreme physical and chemical conditions of hot ecosystems.
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Santana MM, Portillo MC, Gonzalez JM. Mutualistic growth of the sulfate-reducer Desulfovibrio vulgaris Hildenborough with different carbohydrates. Microbiology (Reading) 2012. [DOI: 10.1134/s002626171206015x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Bücking C, Piepenbrock A, Kappler A, Gescher J. Outer-membrane cytochrome-independent reduction of extracellular electron acceptors in Shewanella oneidensis. Microbiology (Reading) 2012; 158:2144-2157. [DOI: 10.1099/mic.0.058404-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Clemens Bücking
- Institut für angewandte Biowissenschaften, Angewandte Biologie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Annette Piepenbrock
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, D-72076 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, D-72076 Tübingen, Germany
| | - Johannes Gescher
- Institut für angewandte Biowissenschaften, Angewandte Biologie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
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Ma C, Zhuang L, Zhou S, Yang G, Yuan Y, Xu R. Alkaline extracellular reduction: isolation and characterization of an alkaliphilic and halotolerant bacterium, Bacillus pseudofirmus MC02. J Appl Microbiol 2012; 112:883-91. [DOI: 10.1111/j.1365-2672.2012.05276.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Deciphering the electron transport pathway for graphene oxide reduction by Shewanella oneidensis MR-1. J Bacteriol 2011; 193:3662-5. [PMID: 21602337 DOI: 10.1128/jb.00201-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We determined that graphene oxide reduction by Shewanella oneidensis MR-1 requires the Mtr respiratory pathway by analyzing a range of mutants lacking these proteins. Electron shuttling compounds increased the graphene oxide reduction rate 3- to 5-fold. These results may help facilitate the use of bacteria for large-scale graphene production.
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Brigé A, Motte B, Borloo J, Buysschaert G, Devreese B, Van Beeumen JJ. Bacterial decolorization of textile dyes is an extracellular process requiring a multicomponent electron transfer pathway. Microb Biotechnol 2011; 1:40-52. [PMID: 21261820 PMCID: PMC3864430 DOI: 10.1111/j.1751-7915.2007.00005.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Many studies have reported microorganisms as efficient biocatalysts for colour removal of dye-containing industrial wastewaters. We present the first comprehensive study to identify all molecular components involved in decolorization by bacterial cells. Mutants from the model organism Shewanella oneidensis MR-1, generated by random transposon and targeted insertional mutagenesis, were screened for defects in decolorization of an oxazine and diazo dye. We demonstrate that decolorization is an extracellular reduction process requiring a multicomponent electron transfer pathway that consists of cytoplasmic membrane, periplasmic and outer membrane components. The presence of melanin, a redox-active molecule excreted by S. oneidensis, was shown to enhance the dye reduction rates. Menaquinones and the cytochrome CymA are the crucial cytoplasmic membrane components of the pathway, which then branches off via a network of periplasmic cytochromes to three outer membrane cytochromes. The key proteins of this network are MtrA and OmcB in the periplasm and outer membrane respectively. A model of the complete dye reduction pathway is proposed in which the dye molecules are reduced by the outer membrane cytochromes either directly or indirectly via melanin.
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Affiliation(s)
- Ann Brigé
- Department of Biochemistry, Physiology and Microbiology, Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, Ghent, Belgium.
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Atsumi S, Wu TY, Machado IMP, Huang WC, Chen PY, Pellegrini M, Liao JC. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol 2011; 6:449. [PMID: 21179021 PMCID: PMC3018172 DOI: 10.1038/msb.2010.98] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 10/25/2010] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli has been engineered to produce isobutanol, with titers reaching greater than the toxicity level. However, the specific effects of isobutanol on the cell have never been fully understood. Here, we aim to identify genotype–phenotype relationships in isobutanol response. An isobutanol-tolerant mutant was isolated with serial transfers. Using whole-genome sequencing followed by gene repair and knockout, we identified five mutations (acrA, gatY, tnaA, yhbJ, and marCRAB) that were primarily responsible for the increased isobutanol tolerance. We successfully reconstructed the tolerance phenotype by combining deletions of these five loci, and identified glucosamine-6-phosphate as an important metabolite for isobutanol tolerance, which presumably enhanced membrane synthesis. The isobutanol-tolerant mutants also show increased tolerance to n-butanol and 2-methyl-1-butanol, but showed no improvement in ethanol tolerance and higher sensitivity to hexane and chloramphenicol than the parental strain. These results suggest that C4, C5 alcohol stress impacts the cell differently compared with the general solvent or antibiotic stresses. Interestingly, improved isobutanol tolerance did not increase the final titer of isobutanol production.
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Affiliation(s)
- Shota Atsumi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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Gerlach R, Field EK, Viamajala S, Peyton BM, Apel WA, Cunningham AB. Influence of carbon sources and electron shuttles on ferric iron reduction by Cellulomonas sp. strain ES6. Biodegradation 2011; 22:983-95. [PMID: 21318474 DOI: 10.1007/s10532-011-9457-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 01/31/2011] [Indexed: 11/26/2022]
Abstract
Microbially reduced iron minerals can reductively transform a variety of contaminants including heavy metals, radionuclides, chlorinated aliphatics, and nitroaromatics. A number of Cellulomonas spp. strains, including strain ES6, isolated from aquifer samples obtained at the U.S. Department of Energy's Hanford site in Washington, have been shown to be capable of reducing Cr(VI), TNT, natural organic matter, and soluble ferric iron [Fe(III)]. This research investigated the ability of Cellulomonas sp. strain ES6 to reduce solid phase and dissolved Fe(III) utilizing different carbon sources and various electron shuttling compounds. Results suggest that Fe(III) reduction by and growth of strain ES6 was dependent upon the type of electron donor, the form of iron present, and the presence of synthetic or natural organic matter, such as anthraquinone-2,6-disulfonate (AQDS) or humic substances. This research suggests that Cellulomonas sp. strain ES6 could play a significant role in metal reduction in the Hanford subsurface and that the choice of carbon source and organic matter addition can allow for independent control of growth and iron reduction activity.
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Affiliation(s)
- Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
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Role of Geobacter sulfurreducens outer surface c-type cytochromes in reduction of soil humic acid and anthraquinone-2,6-disulfonate. Appl Environ Microbiol 2010; 76:2371-5. [PMID: 20154112 DOI: 10.1128/aem.02250-09] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.
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Chee-Sanford JC, Mackie RI, Koike S, Krapac IG, Lin YF, Yannarell AC, Maxwell S, Aminov RI. Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. JOURNAL OF ENVIRONMENTAL QUALITY 2009; 38:1086-108. [PMID: 19398507 DOI: 10.2134/jeq2008.0128] [Citation(s) in RCA: 463] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.
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Jiao L, Lu H, Zhou J, Wang J. Quinone-mediated decolorization of sulfonated azo dyes by cells and cell extracts from Sphingomonas xenophaga. J Environ Sci (China) 2009; 21:503-508. [PMID: 19634426 DOI: 10.1016/s1001-0742(08)62299-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The effects of various quinone compounds on the decolorization rates of sulfonated azo dyes by Sphingomonas xenophaga QYY were investigated. The results showed that anthraquinone-2-sulfonate (AQS) was the most effective redox mediator and AQS reduction was the rate-limited step of AQS-mediated decolorization of sulfonated azo dyes. Based on AQS biological toxicity tests, it was assumed that AQS might enter the cells and kill them. In the cytoplasmic extracts from strain QYY, AQS more effectively increased decolorization rates of sulfonated azo dyes than other quinone compounds. In addition, we found a NADH/FMN-dependent AQS reductase using nondenaturing polyacrylamide gel electrophoresis (Native-PAGE).
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Affiliation(s)
- Ling Jiao
- School of Environmental and Biological Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian 116024, China.
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37
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Newman DK. From iron oxides to infections. CHEMSUSCHEM 2009; 2:380-382. [PMID: 19408265 DOI: 10.1002/cssc.200900038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cellular electron transfer under diverse anaerobic conditions is a primary topic of research conducted by the Newman group. In this Viewpoint, a summary is given of how a geobiological approach has been used to investigate these processes.
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Affiliation(s)
- Dianne K Newman
- Departments of Biology and Earth and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave. 68-380, Cambridge, MA 02139-4307, USA.
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38
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Zgurskaya HI, Yamada Y, Tikhonova EB, Ge Q, Krishnamoorthy G. Structural and functional diversity of bacterial membrane fusion proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:794-807. [PMID: 19041958 DOI: 10.1016/j.bbapap.2008.10.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/21/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
Abstract
Membrane Fusion Proteins (MFPs) are functional subunits of multi-component transporters that perform diverse physiological functions in both Gram-positive and Gram-negative bacteria. MFPs associate with transporters belonging to Resistance-Nodulation-cell Division (RND), ATP-Binding Cassette (ABC) and Major Facilitator (MF) superfamilies of proteins. Recent studies suggested that MFPs interact with substrates and play an active role in transport reactions. In addition, the MFP-dependent transporters from Gram-negative bacteria recruit the outer membrane channels to expel various substrates across the outer membrane into external medium. This review is focused on the diversity, structure and molecular mechanism of MFPs that function in multidrug efflux. Using phylogenetic approaches we analyzed diversity and representation of multidrug MFPs in sequenced bacterial genomes. In addition to previously characterized MFPs from Gram-negative bacteria, we identified MFPs that associate with RND-, MF- and ABC-type transporters in Gram-positive bacteria. Sequence analyses showed that MFPs vary significantly in size (200-650 amino acid residues) with some of them lacking the signature alpha-helical domain of multidrug MFPs. Furthermore, many transport operons contain two- or three genes encoding distinct MFPs. We further discuss the diversity of MFPs in the context of current views on the mechanism and structure of MFP-dependent transporters.
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Affiliation(s)
- Helen I Zgurskaya
- University of Oklahoma Department of Chemistry and Biochemistry 620 Parrington Oval, Room 208 Norman, OK 73019, USA.
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Mechanism and Consequences of anaerobic respiration of cobalt by Shewanella oneidensis strain MR-1. Appl Environ Microbiol 2008; 74:6880-6. [PMID: 18836009 DOI: 10.1128/aem.00840-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria from the genus Shewanella are the most diverse respiratory organisms studied to date and can utilize a variety of metals and metal(loid)s as terminal electron acceptors. These bacteria can potentially be used in bioremediation applications since the redox state of metals often influences both solubility and toxicity. Understanding molecular mechanisms by which metal transformations occur and the consequences of by-products that may be toxic to the organism and thus inhibitory to the overall process is significant to future applications for bioremediation. Here, we examine the ability of Shewanella oneidensis to catalyze the reduction of chelated cobalt. We describe an unexpected ramification of [Co(III)-EDTA](-) reduction by S. oneidensis: the formation of a toxic by-product. We found that [Co(II)-EDTA](2-), the product of [Co(III)-EDTA](-) respiration, inhibited the growth of S. oneidensis strain MR-1 and that this toxicity was partially abolished by the addition of MgSO(4). We demonstrate that [Co(III)-EDTA](-) reduction by S. oneidensis requires the Mtr extracellular respiratory pathway and associated pathways required to develop functional Mtr enzymes (the c-type cytochrome maturation pathway) and ensure proper localization (type II secretion). The Mtr pathway is known to be required for a variety of substrates, including some chelated and insoluble metals and organic compounds. Understanding the full substrate range for the Mtr pathway is crucial for developing S. oneidensis strains as a tool for bioremediation.
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O'Loughlin EJ. Effects of electron transfer mediators on the bioreduction of lepidocrocite (gamma-FeOOH) by Shewanella putrefaciens CN32. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:6876-6882. [PMID: 18853803 DOI: 10.1021/es800686d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Electron transfer mediators (ETMs) such as low-molecular-mass quinones (e.g., juglone and lawsone) and humic substances are believed to play a role in many redox reactions involved in contaminant transformations and the biogeochemical cycling of many redox-active elements (e.g., Fe and Mn) in aquatic and terrestrial environments. This study examines the effects of a series of compounds representing major classes of natural and synthetic organic ETMs, including low-molecular-mass quinones, humic substances, phenazines, phenoxazines, phenothiazines, and indigo derivatives, on the bioreduction of lepidocrocite (gamma-FeOOH) by the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens CN32. Although S. putrefaciens CN32 was able to reduce lepidocrocite in the absence of exogenous ETMs, the addition of exogenous ETMs enhanced the bioreduction of lepidocrocite. In general, the rate of Fe(II) production correlated well with the reduction potentials of the ETMs. The addition of humic acids or unfractionated natural organic matter at concentrations of 10 mg organic CL(-1) resulted in, at best, a minimal enhancement of lepidocrocite bioreduction. This observation suggests that electron shuttling by humic substances is not likely to play a major role in Fe(lll) bioreduction in oligotrophic environments such as subsurface sediments with low organic C contents.
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Affiliation(s)
- Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-4843, USA.
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41
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Affiliation(s)
- D K Newman
- Department of Biology and Earth & Planetary Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue 68-380, Cambridge, MA 02139-4307, USA.
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Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl Environ Microbiol 2008; 74:2646-58. [PMID: 18344346 PMCID: PMC2394881 DOI: 10.1128/aem.01656-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 03/02/2008] [Indexed: 01/06/2023] Open
Abstract
Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O(2) concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.
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Affiliation(s)
- Gregory J Dick
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Sciences University, 20000 NW Walker Rd., Beaverton, OR 97006, USA
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Ross DE, Ruebush SS, Brantley SL, Hartshorne RS, Clarke TA, Richardson DJ, Tien M. Characterization of protein-protein interactions involved in iron reduction by Shewanella oneidensis MR-1. Appl Environ Microbiol 2007; 73:5797-808. [PMID: 17675441 PMCID: PMC2074908 DOI: 10.1128/aem.00146-07] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interaction of proteins implicated in dissimilatory metal reduction by Shewanella oneidensis MR-1 (outer membrane [OM] proteins OmcA, MtrB, and MtrC; OM-associated protein MtrA; periplasmic protein CctA; and cytoplasmic membrane protein CymA) were characterized by protein purification, analytical ultracentrifugation, and cross-linking methods. Five of these proteins are heme proteins, OmcA (83 kDa), MtrC (75 kDa), MtrA (32 kDa), CctA (19 kDa), and CymA (21 kDa), and can be visualized after sodium dodecyl sulfate-polyacrylamide gel electrophoresis by heme staining. We show for the first time that MtrC, MtrA, and MtrB form a 198-kDa complex with a 1:1:1 stoichiometry. These proteins copurify through anion-exchange chromatography, and the purified complex has the ability to reduce multiple forms of Fe(III) and Mn(IV). Additionally, MtrA fractionates with the OM through sucrose density gradient ultracentrifugation, and MtrA comigrates with MtrB in native gels. Protein cross-linking of whole cells with 1% formaldehyde show new heme bands of 160, 151, 136, and 59 kDa. Using antibodies to detect each protein separately, heme proteins OmcA and MtrC were shown to cross-link, yielding the 160-kDa band. Consistent with copurification results, MtrB cross-links with MtrA, forming high-molecular-mass bands of approximately 151 and 136 kDa.
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Affiliation(s)
- Daniel E Ross
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
Although it has long been known that microbes can generate energy using diverse strategies, only recently has it become clear that a growing number involve electron transfer to or from extracellular substrates. The best-known example of what we will term 'extracellular respiration' is electron transfer between microbes and minerals, such as iron and manganese (hydr)oxides. This makes sense, given that these minerals are sparingly soluble. What is perhaps surprising, however, is that a number of substrates that might typically be classified as 'soluble' are also respired at the cell surface. There are several reasons why this might be the case: the substrate, in its ecological context, might be associated with a solid surface and thus effectively insoluble; the substrate, while soluble, might simply be too large to transport inside the cell; or the substrate, while benign in one redox state, might become toxic after it is metabolized. In this review, we discuss various examples of extracellular respiration, paying particular attention to what is known about the molecular mechanisms underlying these processes. As will become clear, much remains to be learned about the biochemistry, cell biology and regulation of extracellular respiration, making it a rich field of study for molecular microbiologists.
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Affiliation(s)
- Jeffrey A Gralnick
- Department of Microbiology, University of Minnesota, Saint Paul, MN, USA.
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Groh JL, Luo Q, Ballard JD, Krumholz LR. Genes that enhance the ecological fitness of Shewanella oneidensis MR-1 in sediments reveal the value of antibiotic resistance. Appl Environ Microbiol 2006; 73:492-8. [PMID: 17114320 PMCID: PMC1796991 DOI: 10.1128/aem.01086-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental bacteria persist in various habitats, yet little is known about the genes that contribute to growth and survival in their respective ecological niches. Signature-tagged mutagenesis (STM) of Shewanella oneidensis MR-1 coupled with a screen involving incubations of mutant strains in anoxic aquifer sediments allowed us to identify 47 genes that enhance fitness in sediments. Gene functions inferred from annotations provide us with insight into physiological and ecological processes that environmental bacteria use while growing in sediment ecosystems. Identification of the mexF gene and other potential membrane efflux components by STM demonstrated that homologues of multidrug resistance genes present in pathogens are required for sediment fitness of nonpathogenic bacteria. Further studies with a mexF deletion mutant demonstrated that the multidrug resistance pump encoded by mexF is required for resistance to antibiotics, including chloramphenicol and tetracycline. Chloramphenicol-adapted cultures exhibited mutations in the gene encoding a TetR family regulatory protein, indicating a role for this protein in regulating expression of the mexEF operon. The relative importance of mexF for sediment fitness suggests that antibiotic efflux may be a required process for bacteria living in sediment systems.
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Affiliation(s)
- Jennifer L Groh
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
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Ruebush SS, Brantley SL, Tien M. Reduction of soluble and insoluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions. Appl Environ Microbiol 2006; 72:2925-35. [PMID: 16597999 PMCID: PMC1449039 DOI: 10.1128/aem.72.4.2925-2935.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of iron substrates and growth conditions on in vitro dissimilatory iron reduction by membrane fractions of Shewanella oneidensis MR-1 was characterized. Membrane fractions were separated by sucrose density gradients from cultures grown with O(2), fumarate, and aqueous ferric citrate as the terminal electron acceptor. Marker enzyme assays and two-dimensional gel electrophoresis demonstrated the high degree of separation between the outer and cytosolic membrane. Protein expression pattern was similar between chelated iron- and fumarate-grown cultures, but dissimilar for oxygen-grown cultures. Formate-dependent ferric reductase activity was assayed with citrate-Fe(3+), ferrozine-Fe(3+), and insoluble goethite as electron acceptors. No activity was detected in aerobic cultures. For fumarate and chelated iron-grown cells, the specific activity for the reduction of soluble iron was highest in the cytosolic membrane. The reduction of ferrozine-Fe(3+) was greater than the reduction of citrate-Fe(3+). With goethite, the specific activity was highest in the total membrane fraction (containing both cytosolic and outer membrane), indicating participation of the outer membrane components in electron flow. Heme protein content and specific activity for iron reduction was highest with chelated iron-grown cultures with no heme proteins in aerobically grown membrane fractions. Western blots showed that CymA, a heme protein involved in iron reduction, expression was also higher in iron-grown cultures compared to fumarate- or aerobic-grown cultures. To study these processes, it is important to use cultures grown with chelated Fe(3+) as the electron acceptor and to assay ferric reductase activity using goethite as the substrate.
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Affiliation(s)
- Shane S Ruebush
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, Pennsylvania State University, University Park, PA 16802, USA
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Gralnick JA, Vali H, Lies DP, Newman DK. Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1. Proc Natl Acad Sci U S A 2006; 103:4669-74. [PMID: 16537430 PMCID: PMC1450229 DOI: 10.1073/pnas.0505959103] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shewanella species are renowned for their respiratory versatility, including their ability to respire poorly soluble substrates by using enzymatic machinery that is localized to the outside of the cell. The ability to engage in "extracellular respiration" to date has focused primarily on respiration of minerals. Here, we identify two gene clusters in Shewanella oneidensis strain MR-1 that each contain homologs of genes required for metal reduction and genes that are predicted to encode dimethyl sulfoxide (DMSO) reductase subunits. Molecular and genetic analyses of these clusters indicate that one (SO1427-SO1432) is required for anaerobic respiration of DMSO. We show that DMSO respiration is an extracellular respiratory process through the analysis of mutants defective in type II secretion, which is required for transporting proteins to the outer membrane in Shewanella. Moreover, immunogold labeling of DMSO reductase subunits reveals that they reside on the outer leaflet of the outer membrane under anaerobic conditions. The extracellular localization of the DMSO reductase in S. oneidensis suggests these organisms may perceive DMSO in the environment as an insoluble compound.
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Affiliation(s)
- Jeffrey A Gralnick
- Divisions of Geological and Planetary Sciences and Biology, and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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Van Trump JI, Sun Y, Coates JD. Microbial Interactions with Humic Substances1. ADVANCES IN APPLIED MICROBIOLOGY 2006; 60:55-96. [PMID: 17157633 DOI: 10.1016/s0065-2164(06)60003-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- J Ian Van Trump
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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Bencheikh-Latmani R, Williams SM, Haucke L, Criddle CS, Wu L, Zhou J, Tebo BM. Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction. Appl Environ Microbiol 2005; 71:7453-60. [PMID: 16269787 PMCID: PMC1287662 DOI: 10.1128/aem.71.11.7453-7460.2005] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome DNA microarrays were used to examine the gene expression profile of Shewanella oneidensis MR-1 during U(VI) and Cr(VI) reduction. The same control, cells pregrown with nitrate and incubated with no electron acceptor, was used for the two time points considered and for both metals. U(VI)-reducing conditions resulted in the upregulation (> or = 3-fold) of 121 genes, while 83 genes were upregulated under Cr(VI)-reducing conditions. A large fraction of the genes upregulated [34% for U(VI) and 29% for Cr(VI)] encode hypothetical proteins of unknown function. Genes encoding proteins known to reduce alternative electron acceptors [fumarate, dimethyl sulfoxide, Mn(IV), or soluble Fe(III)] were upregulated under both U(VI)- and Cr(VI)-reducing conditions. The involvement of these upregulated genes in the reduction of U(VI) and Cr(VI) was tested using mutants lacking one or several of the gene products. Mutant testing confirmed the involvement of several genes in the reduction of both metals: mtrA, mtrB, mtrC, and menC, all of which are involved in Fe(III) citrate reduction by MR-1. Genes encoding efflux pumps were upregulated under Cr(VI)- but not under U(VI)-reducing conditions. Genes encoding proteins associated with general (e.g., groL and dnaJ) and membrane (e.g., pspBC) stress were also upregulated, particularly under U(VI)-reducing conditions, pointing to membrane damage by the solid-phase reduced U(IV) and Cr(III) and/or the direct effect of the oxidized forms of the metals. This study sheds light on the multifaceted response of MR-1 to U(VI) and Cr(VI) under anaerobic conditions and suggests that the same electron transport pathway can be used for more than one electron acceptor.
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Affiliation(s)
- Rizlan Bencheikh-Latmani
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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Beliaev AS, Klingeman DM, Klappenbach JA, Wu L, Romine MF, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J. Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J Bacteriol 2005; 187:7138-45. [PMID: 16199584 PMCID: PMC1251602 DOI: 10.1128/jb.187.20.7138-7145.2005] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. Several groups of genes exhibited elevated expression levels in the presence of metals, including those encoding putative multidrug efflux transporters, detoxification proteins, extracytoplasmic sigma factors and PAS-domain regulators. Only one of the 42 predicted c-type cytochromes in MR-1, SO3300, displayed significantly elevated transcript levels across all metal-reducing conditions. Genes encoding decaheme cytochromes MtrC and MtrA that were previously linked to the reduction of different forms of Fe(III) and Mn(IV), exhibited only slight decreases in relative mRNA abundances under metal-reducing conditions. In contrast, specific transcriptome responses were displayed to individual non-metal electron acceptors resulting in the identification of unique groups of nitrate-, thiosulfate- and TMAO-induced genes including previously uncharacterized multi-cytochrome gene clusters. Collectively, the gene expression results reflect the fundamental differences between metal and non-metal respiratory pathways of S. oneidensis MR-1, where the coordinate induction of detoxification and stress response genes play a key role in adaptation of this organism under metal-reducing conditions. Moreover, the relative paucity and/or the constitutive nature of genes involved in electron transfer to metals is likely due to the low-specificity and the opportunistic nature of the metal-reducing electron transport pathways.
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Affiliation(s)
- A S Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MS P7-50, Richland, Washington 99352, USA.
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