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Hou L, Zheng B, Jiang Z, Hu Y, Shi L, Dong Y, Jiang Y. The dmsEFABGH operon encodes an essential and modular electron transfer pathway for extracellular iodate reduction by Shewanella oneidensis MR-1. Microbiol Spectr 2024; 12:e0051224. [PMID: 38916364 PMCID: PMC11302344 DOI: 10.1128/spectrum.00512-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Extracellular iodate reduction by Shewanella spp. contributes to iodide generation in the biogeochemical cycling of iodine. However, there is a disagreement on whether Shewanella spp. use different extracellular electron transfer pathways with dependence on electron donors in iodate reduction. In this study, a series of gene deletion mutants of Shewanella oneidensis MR-1 were created to investigate the roles of dmsEFABGH, mtrCAB, and so4357-so4362 operons in iodate reduction. The iodate-reducing activity of the mutants was tested with lactate, formate, and H2 as the sole electron donors, respectively. In the absence of single-dms gene, iodate reduction efficiency of the mutants was only 12.9%-84.0% with lactate at 24 hours, 22.1%-85.9% with formate at 20 hours, and 19.6%-57.7% with H2 at 42 hours in comparison to complete reduction by the wild type. Progressive inhibition of iodate reduction was observed when the dms homolog from the so4357-so4362 operon was deleted in the single-dms gene mutants. This result revealed complementation of dmsEFABGH by so4357-so4362 at the single-gene level, indicating modularity of the extracellular electron transfer pathway encoded by dmsEFABGH operon. Under the conditions of all electron donors, significant inhibition of iodate reduction and accumulation of H2O2 were detected for ΔmtrCAB. Collectively, these results demonstrated that the dmsEFABGH operon encodes an essential and modular iodate-reducing pathway without electron donor dependence in S. oneidensis MR-1. The mtrCAB operon was involved in H2O2 elimination with all electron donors. The findings in this study improved the understanding of molecular mechanisms underlying extracellular iodate reduction.IMPORTANCEIodine is an essential trace element for human and animals. Recent studies revealed the contribution of microbial extracellular reduction of iodate in biogeochemical cycling of iodine. Multiple reduced substances can be utilized by microorganisms as energy source for iodate reduction. However, varied electron transfer pathways were proposed for iodate reduction with different electron donors in the model strain Shewanella oneidensis MR-1. Here, through a series of gene deletion and iodate reduction experiments, we discovered that the dmsEFABGH operon was essential for iodate reduction with at least three electron donors, including lactate, formate, and H2. The so4357-so4362 operon was first demonstrated to be capable of complementing the function of dmsEFABGH at single-gene level.
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Affiliation(s)
- Lingyu Hou
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Beiling Zheng
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Eco-Restoration, Wuhan, Hubei, China
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2
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Bhaduri S, Behera M. Advancement in constructed wetland microbial fuel cell process for wastewater treatment and electricity generation: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34574-2. [PMID: 39102132 DOI: 10.1007/s11356-024-34574-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024]
Abstract
The constructed wetland coupled with a microbial fuel cell (CW-MFC) is a wastewater treatment process that combines contaminant removal with electricity production, making it an environmentally friendly option. This hybrid system primarily relies on anaerobic bioprocesses for wastewater treatment, although other processes such as aerobic bioprocesses, plant uptake, and chemical oxidation also contribute to the removal of organic matter and nutrients. CW-MFCs have been successfully used to treat various types of wastewater, including urban, pharmaceutical, paper and pulp industry, metal-contaminated, and swine wastewater. In CW-MFC, macrophytes such as rice plants, Spartina angalica, Canna indica, and Phragmites australis are used. The treatment process can achieve a chemical oxygen demand removal rate of between 80 and 100%. Initially, research focused on enhancing power generation from CW-MFC, but recent studies have shifted towards resource recovery from wastewater. This review paper provides an overview of the development of constructed wetland microbial fuel cell technology, from its early stages to its current applications. The paper also highlights research gaps and potential directions for future research.
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Affiliation(s)
- Soumyadeep Bhaduri
- School of Infrastructure, Indian Institute of Technology Bhubaneswar, Odisha, 752050, India
| | - Manaswini Behera
- School of Infrastructure, Indian Institute of Technology Bhubaneswar, Odisha, 752050, India.
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Tu W, Thompson IP, Huang WE. Engineering bionanoreactor in bacteria for efficient hydrogen production. Proc Natl Acad Sci U S A 2024; 121:e2404958121. [PMID: 38985767 PMCID: PMC11260135 DOI: 10.1073/pnas.2404958121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024] Open
Abstract
Hydrogen production through water splitting is a vital strategy for renewable and sustainable clean energy. In this study, we developed an approach integrating nanomaterial engineering and synthetic biology to establish a bionanoreactor system for efficient hydrogen production. The periplasmic space (20 to 30 nm) of an electroactive bacterium, Shewanella oneidensis MR-1, was engineered to serve as a bionanoreactor to enhance the interaction between electrons and protons, catalyzed by hydrogenases for hydrogen generation. To optimize electron transfer, we used the microbially reduced graphene oxide (rGO) to coat the electrode, which improved the electron transfer from the electrode to the cells. Native MtrCAB protein complex on S. oneidensis and self-assembled iron sulfide (FeS) nanoparticles acted in tandem to facilitate electron transfer from an electrode to the periplasm. To enhance proton transport, S. oneidensis MR-1 was engineered to express Gloeobacter rhodopsin (GR) and the light-harvesting antenna canthaxanthin. This led to efficient proton pumping when exposed to light, resulting in a 35.6% increase in the rate of hydrogen production. The overexpression of native [FeFe]-hydrogenase further improved the hydrogen production rate by 56.8%. The bionanoreactor engineered in S. oneidensis MR-1 achieved a hydrogen yield of 80.4 μmol/mg protein/day with a Faraday efficiency of 80% at a potential of -0.75 V. This periplasmic bionanoreactor combines the strengths of both nanomaterial and biological components, providing an efficient approach for microbial electrosynthesis.
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Affiliation(s)
- Weiming Tu
- Department of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Ian P. Thompson
- Department of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
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4
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Jiang Y, Dong Y, Sui M, Yu J, Wu J, Fu D. Towards a new understanding of bioelectrochemical systems from the perspective of microecosystems: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168410. [PMID: 37939951 DOI: 10.1016/j.scitotenv.2023.168410] [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: 09/06/2023] [Revised: 11/04/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
Bioelectrochemical system (BES) holds promise for sustainable energy generation and wastewater treatment. The microbial communities, as the core of BES, play a crucial role in its performance, thus needing to be systematically studied. However, researches considering microbial communities in BES from an ecological perspective are limited. This review provided a comprehensive summary of the BES with special emphasis on microecological principles, commencing with the dynamic formation and succession of the microbial communities. It also clarified the intricate interspecies relationships and quorum-sensing mechanisms regulated by dominant species. Furthermore, this review addressed the crucial themes in BES-related researches on ecological processes, including growth patterns, ecological structures, and defense strategies against external disturbances. By offering this novel perspective, it would contribute to enhancing the understanding of BES-centered technologies and facilitating future research in this field.
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Affiliation(s)
- Yiying Jiang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yue Dong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Mingrui Sui
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China.
| | - Jimeng Yu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jiaxin Wu
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China
| | - Daxuan Fu
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China
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5
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Chu G, Wang W, Dou Y, Sun K, Qin W, Wang Z, Si Y. Enhanced microbial degradation mediated by pyrogenic carbon toward p-nitrophenol: Role of carbon structures and iron minerals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165797. [PMID: 37506896 DOI: 10.1016/j.scitotenv.2023.165797] [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: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
Pyrogenic carbon (PC) including black carbons and engineered carbons can mediate the extracellular electron transfer to facilitate the biogeochemical reaction with organic pollutants. Yet, the role of carbon structures and iron minerals on PC-mediated microbial degradation is still lacking of understanding. Herein, we studied the electrochemical properties of PCs produced from varied feedstock with regards to the mediated degradation of p-nitrophenol (PNP) by Shewanella putrefaciens CN32 in anoxic system. Mediated degradation by PCs was enhanced by facilitating extracellular electron transfer through oxygenated group and graphitic structure. Graphitic crystallites improved the electron-accepting capacity (as suggested by ID/IG and EAC) and diminished the electrochemical impedance (as suggested by Rct), contributing to PNP degradation under the anoxic system. Furthermore, more interfacial adsorption was conducive to the mediated reduction by the graphitic structure on PCs of high-temperature. In the presence of iron minerals, both hematite and goethite significantly facilitated PC-mediated degradation, which could be ascribed to the enhancement of the electron-donating capacity of microorganism and the accumulation of the reductive-state PCs by the interaction with generated Fe(II). This work paves a feasible way to the technical design on the remediation of phenolic contaminants by PC-mediated microbial degradation in environment.
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Affiliation(s)
- Gang Chu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China; Yunnan Provincial Key Laboratory of Carbon Sequestration and Pollution Control in Soils, Faculty of Environment Science & Engineering, Kunming University of Science & Technology, Kunming 650500, Yunnan, China.
| | - Wangmin Wang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yang Dou
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Kai Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Wenxiu Qin
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Zhen Wang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Youbin Si
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Faculty of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China.
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Rastkhah E, Fatemi F, Maghami P. Optimizing the Metal Bioreduction Process in Recombinant Shewanella azerbaijanica Bacteria: A Novel Approach via mtrC Gene Cloning and Nitrate-Reducing Pathway Destruction. Mol Biotechnol 2023:10.1007/s12033-023-00920-x. [PMID: 37917324 DOI: 10.1007/s12033-023-00920-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/22/2023] [Indexed: 11/04/2023]
Abstract
Environmental pollution is growing every day in terms of the increase in population, industrialization, and urbanization. Shewanella azerbaijanica is introduced as a highly potent bacterium in metal bioremediation. The mtrC gene was selected as a cloning target to improve electron flux chains in the EET (extracellular electron transfer) pathway. Using the SDM (site-directed mutagenesis) technique, the unique gene assembly featured the mtrC gene sandwiched between two napD/B genes to disrupt the nitrate reduction pathway, which serves as the primary metal reduction competitor. Shew-mtrC gene construction was transferred to expression plasmid pET28a (+) in the expression host bacteria (E. coli BL21 and S. azerbaijanica), in pUC57, cloning plasmid, which was transferred to the cloning host bacteria E. coli Top10 and S. azerbaijanica. All cloning procedures (i.e., synthesis, insertion, transformation, cloning, and protein expression) were verified and confirmed by precise tests. ATR-FTIR analysis, CD, western blotting, affinity chromatography, SDS-PAGE, and other techniques were used to confirm the expression and structure of the MtrC protein. The genome sequence and primers were designed according to the submitted Shewanella oneidensis MR-1 genome, the most similar bacteria to this native species. The performance of recombinant S. azerbaijanica bacterium in metal bioremediation, as sustainable strategy, has to be verified by more research.
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Affiliation(s)
- Elham Rastkhah
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faezeh Fatemi
- Nuclear Fuel Cycle Research School, Nuclear Science and Technology Research Institute, Tehran, Iran.
| | - Parvaneh Maghami
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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7
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Sun W, Xu Y, Liang Y, Yu Q, Gao H. A novel bacterial sulfite dehydrogenase that requires three c-type cytochromes for electron transfer. Appl Environ Microbiol 2023; 89:e0110823. [PMID: 37732808 PMCID: PMC10617556 DOI: 10.1128/aem.01108-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
c-type Cytochromes (c-Cyts), primarily as electron carriers and oxidoreductases, play a key role in energy transduction processes in virtually all living organisms. Many bacteria, such as Shewanella oneidensis, are particularly rich in c-Cyts, supporting respiratory versatility not seen in eukaryotes. Unfortunately, a large number of c-Cyts are underexplored, and their biological functions remain unknown. In this study, we identify SorCABD of S. oneidensis as a novel sulfite dehydrogenase (SDH), which catalyzes the oxidation of sulfite to sulfate. In addition to catalytic subunit SorA, this enzymatic complex includes three c-Cyt subunits, which all together carry out electron transfer. The electrons extracted from sulfite oxidation are ultimately delivered to oxygen, leading to oxygen reduction, a process relying on terminal oxidase cyt cbb3. Genomic analysis suggests that the homologs of this SDH are present in a small number of bacterial genera, Shewanella and Vibrio in particular. Because these bacteria are generally capable of reducing sulfite under anaerobic conditions, the co-existence of a sulfite oxidation system implies that they may play especially important roles in the transformation of sulfur species in natural environments.Importancec-type Cytochromes (c-Cyts) endow bacteria with high flexibility in their oxidative/respiratory systems, allowing them to extracellularly transform diverse inorganic and organic compounds for survival and growth. However, a large portion of the bacterial c-Cyts remain functionally unknown. Here, we identify three c-Cyts that work together as essential electron transfer partners for the catalytic subunit of a novel SDH in sulfite oxidation in Shewanella oneidensis. This characteristic makes S. oneidensis the first organism known to be capable of oxidizing and reducing sulfite. The findings suggest that Shewanella, along with a small number of other aquatic bacteria, would serve as a particular driving force in the biogeochemical sulfur cycle in nature.
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Affiliation(s)
- Weining Sun
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuanyou Xu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yawen Liang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingzi Yu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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8
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Han S, Guo K, Wang W, Tao YJ, Gao H. Bacterial TANGO2 homologs are heme-trafficking proteins that facilitate biosynthesis of cytochromes c. mBio 2023; 14:e0132023. [PMID: 37462360 PMCID: PMC10470608 DOI: 10.1128/mbio.01320-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 09/02/2023] Open
Abstract
Heme, an essential molecule for virtually all living organisms, acts primarily as a cofactor in a large number of proteins. However, how heme is mobilized from the site of synthesis to the locations where hemoproteins are assembled remains largely unknown in cells, especially bacterial ones. In this study, with Shewanella oneidensis as the model, we identified HtpA (SO0126) as a heme-trafficking protein and homolog of TANGO2 proteins found in eukaryotes. We showed that HtpA homologs are widely distributed in all domains of living organisms and have undergone parallel evolution. In its absence, the cytochrome (cyt) c content and catalase activity decreased significantly. We further showed that both HtpA and representative TANGO2 proteins bind heme with 1:1 stoichiometry and a relatively low dissociation constant. Protein interaction analyses substantiated that HtpA directly interacts with the cytochrome c maturation system. Our findings shed light on cross-membrane transport of heme in bacteria and extend the understanding of TANGO2 proteins. IMPORTANCE The intracellular trafficking of heme, an essential cofactor for hemoproteins, remains underexplored even in eukaryotes, let alone bacteria. Here we developed a high-throughput method by which HtpA, a homolog of eukaryotic TANGO2 proteins, was identified to be a heme-binding protein that enhances cytochrome c biosynthesis and catalase activity in Shewanella oneidensis. HtpA interacts with the cytochrome c biosynthesis system directly, supporting that this protein, like TANGO2, functions in intracellular heme trafficking. HtpA homologs are widely distributed, but a large majority of them were found to be non-exchangeable, likely a result of parallel evolution. By substantiating the heme-trafficking nature of HtpA and its eukaryotic homologs, our findings provide general insight into the heme-trafficking process and highlight the functional conservation along evolution in all living organisms.
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Affiliation(s)
- Sirui Han
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kailun Guo
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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9
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Chen C, Hamza I. Notes from the Underground: Heme Homeostasis in C. elegans. Biomolecules 2023; 13:1149. [PMID: 37509184 PMCID: PMC10377359 DOI: 10.3390/biom13071149] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Heme is an iron-containing tetrapyrrole that plays a critical role in various biological processes, including oxygen transport, electron transport, signal transduction, and catalysis. However, free heme is hydrophobic and potentially toxic to cells. Organisms have evolved specific pathways to safely transport this essential but toxic macrocycle within and between cells. The bacterivorous soil-dwelling nematode Caenorhabditis elegans is a powerful animal model for studying heme-trafficking pathways, as it lacks the ability to synthesize heme but instead relies on specialized trafficking pathways to acquire, distribute, and utilize heme. Over the past 15 years, studies on this microscopic animal have led to the identification of a number of heme-trafficking proteins, with corresponding functional homologs in vertebrates. In this review, we provide a comprehensive overview of the heme-trafficking proteins identified in C. elegans and their corresponding homologs in related organisms.
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Affiliation(s)
- Caiyong Chen
- MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Iqbal Hamza
- Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
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Wei B, Chen W, Ren X, Wang L, Zhao X. Enhanced Biodegradation of Methyl Orange Through Immobilization of Shewanella oneidensis MR-1 by Polyvinyl Alcohol and Sodium Alginate. Curr Microbiol 2023; 80:272. [PMID: 37410197 DOI: 10.1007/s00284-023-03387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
Shewanella oneidensis MR-1 has great potential for use in remediating azo dye pollution. Here, a new high-efficiency biodegradation method was developed utilizing S. oneidensis MR-1 immobilized by polyvinyl alcohol (PVA) and sodium alginate (SA). After determining the optimal immobilization conditions, the effects of various environmental factors on methyl orange (MO) degradation were analyzed. The biodegradation activity of the immobilized pellets was evaluated by analyzing the MO removal efficiency, and characterization was performed using scanning electron microscopy. The MO adsorption kinetics can be described using pseudo-second-order kinetics. Compared with free bacteria, the MO degradation rate of the immobilized S. oneidensis MR-1 increased from 41% to 92.6% after 21 days, suggesting that the immobilized bacteria performed substantially better and had more stable removal rates. These factors indicate the superiority of bacteria entrapment in addition to its easy application. This study demonstrates that the application of immobilized S. oneidensis MR-1 entrapped by PVA-SA can be used to establish a reactor with stable and high MO removal rates.
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Affiliation(s)
- Buyun Wei
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Wenwen Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xiaoyuan Ren
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Lei Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xueqin Zhao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
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Huang J, Cai XL, Peng JR, Fan YY, Xiao X. Extracellular pollutant degradation feedback regulates intracellular electron transfer process of exoelectrogens: Strategy and mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158630. [PMID: 36084783 DOI: 10.1016/j.scitotenv.2022.158630] [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: 08/08/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Exoelectrogens possess extraordinary degradation ability to various pollutants through extracellular electron transfer (EET). Compared with extracellular electron release process, intracellular electron transfer network is not yet fully recognized. Especially, controversy remains regarding the role of CymA, an essential electron-transfer hub of Shewanella oneidensis MR-1, in EET process. In this study, we thoroughly surveyed the intracellular transfer strategies during EET through dye decolorization. Loss of CymA severely impaired the reduction ability of S. oneidensis MR-1 to methyl orange (MO), but hardly affected the decolorization of aniline blue (AB). Complement of cymA fully restored the MO decolorization ability of ΔcymA mutant. The contribution of CymA to extracellular decolorization was subjected to MO concentrations. The defect in the decolorization ability of ΔcymA mutant was not evident at low MO concentration, but severe at high MO concentration. Further investigation revealed that EET rate determined the significance of CymA in the extracellular bioremediation by S. oneidensis MR-1. Coupled with MO concentrations increasing from 15 to 120 mg/L, the initial electron transfer rates of S. oneidensis MR-1 increased accordingly from 2.69 × 104 to 11.21 × 104 electrons CFU-1 s-1, which led to a gradual increase of the dependencyCymA. Thus, we first revealed that extracellular degradation performance could feedback regulate the intracellular electron transfer process of S. oneidensis MR-1. This work is helpful to fully understand the complex EET process of exoelectrogens and facilitates the application of exoelectrogens in bioremediation of environmental pollutants.
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Affiliation(s)
- Jing Huang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Xin-Lu Cai
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Jie-Ru Peng
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yang-Yang Fan
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China.
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12
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Ding DW, Huang WF, Lei LL, Wu P. Co-fitness analysis identifies a diversity of signal proteins involved in the utilization of specific c-type cytochromes. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01694-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
c-Type cytochromes are essential for extracellular electron transfer (EET) in electroactive microorganisms. The expression of appropriate c-type cytochromes is an important feature of these microorganisms in response to different extracellular electron acceptors. However, how these diverse c-type cytochromes are tightly regulated is still poorly understood.
Methods
In this study, we identified the high co-fitness genes that potentially work with different c-type cytochromes by using genome-wide co-fitness analysis. We also constructed and studied the co-fitness networks that composed of c-type cytochromes and the top 20 high co-fitness genes of them.
Results
We found that high co-fitness genes of c-type cytochromes were enriched in signal transduction processes in Shewanella oneidensis MR-1 cells. We then checked the top 20 co-fitness proteins for each of the 41 c-type cytochromes and identified the corresponding signal proteins for different c-type cytochromes. In particular, through the analysis of the high co-fitness signal protein for CymA, we further confirmed the cooperation between signal proteins and c-type cytochromes and identified a novel signal protein that is putatively involved in the regulation of CymA. In addition, we showed that these signal proteins form two signal transduction modules.
Conclusion
Taken together, these findings provide novel insights into the coordinated utilization of different c-type cytochromes under diverse conditions.
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13
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A Common Target of Nitrite and Nitric Oxide for Respiration Inhibition in Bacteria. Int J Mol Sci 2022; 23:ijms232213841. [PMID: 36430319 PMCID: PMC9697910 DOI: 10.3390/ijms232213841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Nitrite and nitric oxide (NO) are well-known bacteriostatic agents with similar biochemical properties. However, many studies have demonstrated that inhibition of bacterial growth by nitrite is independent of NO. Here, with Shewanella oneidensis as the research model because of its unusually high cytochrome (cyt) c content, we identify a common mechanism by which nitrite and NO compromise cyt c biosynthesis in bacteria, and thereby inhibit respiration. This is achieved by eliminating the inference of the cyclic adenosine monophosphate-catabolite repression protein (cAMP-Crp), a primary regulatory system that controls the cyt c content and whose activity is subjected to the repression of nitrite. Both nitrite and NO impair the CcmE of multiple bacteria, an essential heme chaperone of the System I cyt c biosynthesis apparatus. Given that bacterial targets of nitrite and NO differ enormously and vary even in the same genus, these observations underscore the importance of cyt c biosynthesis for the antimicrobial actions of nitrite and NO.
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14
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Cai X, Zheng X, Wang Y, Tian L, Mao Y. Enhanced Bioremediation Potential of Shewanella decolorationis RNA Polymerase Mutants and Evidence for Novel Azo Dye Biodegradation Pathways. Front Microbiol 2022; 13:843807. [PMID: 35391736 PMCID: PMC8981235 DOI: 10.3389/fmicb.2022.843807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bioremediation has been considered as a promising method for recovering chemical polluted environments. Here Shewanella decolorationis strain Ni1-3 showed versatile abilities in bioremediation. To improve the bioremediation activity, RNA polymerase (RNAP) mutations of strain Ni1-3 were screened. Eleven mutants were obtained, of which mutant #40 showed enhanced Amaranth (AMR) degradation capacity, while mutant #21 showed defected capacity in AMR degradation but greatly enhanced capacity in cathodic metal leaching which is three to four times faster than that of the wild-type (WT) strain Ni1-3, suggesting that different pathways were involved in these two processes. Transcriptional profiling and gene co-expression networks between the mutants (i.e., #40 and #22) and the WT strain disclosed that the non-CymA-Mtr but cytochrome b- and flavin-oxidoreductase-dominated azo dye degradation pathways existed in S. decolorationis, which involved key proteins TorC, TorA, YceJ, YceI, Sye4, etc. Furthermore, the involvement of TorA was verified by trimethylamine N-oxide reduction and molybdenum enzyme inhibitory experiments. This study clearly demonstrates that RNAP mutations are effective to screen active microbial candidates in bioremediation. Meanwhile, by clarifying the novel gene co-expression network of extracellular electron transfer pathways, this study provides new insights in azo dye degradation and broadens the application of Shewanella spp. in bioremediation as well.
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Affiliation(s)
- Xunchao Cai
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China
| | - Xin Zheng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Yicheng Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Li Tian
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
- *Correspondence: Yanping Mao,
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15
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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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16
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Guo K, Feng X, Sun W, Han S, Wu S, Gao H. NapB Restores cytochrome c biosynthesis in bacterial dsbD-deficient mutants. Commun Biol 2022; 5:87. [PMID: 35064202 PMCID: PMC8782879 DOI: 10.1038/s42003-022-03034-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 01/05/2022] [Indexed: 11/10/2022] Open
Abstract
Cytochromes c (cyts c), essential for respiration and photosynthesis in eukaryotes, confer bacteria respiratory versatility for survival and growth in natural environments. In bacteria having a cyt c maturation (CCM) system, DsbD is required to mediate electron transport from the cytoplasm to CcmG of the Ccm apparatus. Here with cyt c-rich Shewanella oneidensis as the research model, we identify NapB, a cyt c per se, that suppresses the CCM defect of a dsbD mutant during anaerobiosis, when NapB is produced at elevated levels, a result of activation by cAMP-Crp. Data are then presented to suggest that NapB reduces CcmG, leading to the suppression. We further show that NapB proteins capable of rescuing CCM in the dsbD mutant form a small distinct clade. The study sheds light on multifunctionality of cyts c, and more importantly, unravels a self-salvation strategy through which bacteria have evolved to better adjust to the natural world. The DsbD protein is normally required for cytochrome c maturation (Ccm) in bacteria. With cytochrome c-rich Shewanella oneidensis as the research model, NapB, the small subunit of the nitrate reductase which is a cytochrome c per se, was found to suppress the Ccm defect resulting from DsbD loss under anaerobic conditions.
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17
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Chen J, Xie P, Huang Y, Gao H. Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide. Int J Mol Sci 2022; 23:979. [PMID: 35055165 PMCID: PMC8780969 DOI: 10.3390/ijms23020979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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Affiliation(s)
| | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (J.C.); (P.X.); (Y.H.)
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18
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Lherbette M, Regeard C, Marlière C, Raspaud E. Biocorrosion on Nanofilms Induces Rapid Bacterial Motions via Iron Dissolution. ACS CENTRAL SCIENCE 2021; 7:1949-1956. [PMID: 34841065 PMCID: PMC8614109 DOI: 10.1021/acscentsci.1c01126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Stability and reactivity of solid metal or mineral surfaces in contact with bacteria are critical properties for development of biocorrosion protection and for understanding bacteria-solid environmental interactions. Here, we opted to work with nanosheets of iron nanolayers offering arbitrarily large and stable areas of contact that can be simply monitored by optical means. We focused our study on the sediments' bacteria, the strain Shewanella oneidensis WT MR-1, that served as models for previous research on electroactivity and iron-reduction effects. Data show that a sudden uniform corrosion appeared after an early electroactive period without specific affinities and that iron dissolution induced rapid bacterial motions. By extending the approach to mutant strains and three bacterial species, we established a correlation between corrosion onset and oxygen-depletion combined with iron reduction and demonstrated bacteria's extraordinary ability to transform their solid environments.
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Affiliation(s)
- Marion Lherbette
- Université
Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Christophe Regeard
- Institute
for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Christian Marlière
- Université
Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Eric Raspaud
- Université
Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
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19
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Sun W, Lin Z, Yu Q, Cheng S, Gao H. Promoting Extracellular Electron Transfer of Shewanella oneidensis MR-1 by Optimizing the Periplasmic Cytochrome c Network. Front Microbiol 2021; 12:727709. [PMID: 34675900 PMCID: PMC8524038 DOI: 10.3389/fmicb.2021.727709] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The low efficiency of extracellular electron transfer (EET) is a major bottleneck for Shewanella oneidensis MR-1 acting as an electroactive biocatalyst in bioelectrochemical systems. Although it is well established that a periplasmic c-type cytochrome (c-Cyt) network plays a critical role in regulating EET efficiency, the understanding of the network in terms of structure and electron transfer activity is obscure and partial. In this work, we attempted to systematically investigate the impacts of the network components on EET in their absence and overproduction individually in microbial fuel cell (MFC). We found that overexpression of c-Cyt CctA leads to accelerated electron transfer between CymA and the Mtr system, which function as the primary quinol oxidase and the outer-membrane (OM) electron hub in EET. In contrast, NapB, FccA, and TsdB in excess severely impaired EET, reducing EET capacity in MFC by more than 50%. Based on the results from both strategies, a series of engineered strains lacking FccA, NapB, and TsdB in combination while overproducing CctA were tested for a maximally optimized c-Cyt network. A strain depleted of all NapB, FccA, and TsdB with CctA overproduction achieved the highest maximum power density in MFCs (436.5 mW/m2), ∼3.62-fold higher than that of wild type (WT). By revealing that optimization of periplasmic c-Cyt composition is a practical strategy for improving EET efficiency, our work underscores the importance in understanding physiological and electrochemical characteristics of c-Cyts involved in EET.
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Affiliation(s)
- Weining Sun
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhufan Lin
- Department of Energy Engineering, State Key Laboratory of Clean Energy, Zhejiang University, Hangzhou, China
| | - Qingzi Yu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shaoan Cheng
- Department of Energy Engineering, State Key Laboratory of Clean Energy, Zhejiang University, Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, China
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20
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Wang Y, Cai X, Mao Y. The first complete genome sequence of species Shewanella decolorationis, from a bioremediation competent strain Ni1-3. G3-GENES GENOMES GENETICS 2021; 11:6326802. [PMID: 34568919 PMCID: PMC8473976 DOI: 10.1093/g3journal/jkab261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/06/2021] [Indexed: 11/12/2022]
Abstract
Shewanella decolorationis are Gram-negative γ-Proteobacteria with environmental bioremediation potential because they can perform anaerobic respiration using various types of pollutants as terminal electron acceptors. So far, three isolated and cultured strains of S. decolorationis have been reported. However, no complete S. decolorationis genome has been published yet, which limited exploring their metabolism and feasibility in application. Here, S. decolorationis Ni1-3 isolated from an electroplating wastewater treatment plant showed strong reduction capabilities on azo dyes and oxidized metals. In order to construct the complete genome, high-quality whole-genome sequencing of strain Ni1-3 were performed by using both Nanopore MinION and Illumina NovaSeq platforms, from which the first complete genome of S. decolorationis was obtained by hybrid assembly. The genome of strain Ni1-3 contains a megaplasmid and a circular chromosome which encodes more proteins than that of the strains LDS1 and S12 belonging to the same species. In addition, more Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are identified in strain Ni1-3 genome. Importantly, 32 cytochrome-c and AzoR azoreductase coding genes are identified in the genome, which make strain Ni1-3 competent to degrade the azo dyes and versatile to bioremediate some other environmental pollution. The complete genome sequence of strain Ni1-3 can expand our knowledge toward its metabolic capabilities and potential, meanwhile, provide a reference to reassemble genomes of other S. decolorationis strains.
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Affiliation(s)
- Yicheng Wang
- Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China
| | - Xunchao Cai
- Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China.,Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen 518071, P.R. China
| | - Yanping Mao
- Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China
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21
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Guo K, Gao H. Physiological Roles of Nitrite and Nitric Oxide in Bacteria: Similar Consequences from Distinct Cell Targets, Protection, and Sensing Systems. Adv Biol (Weinh) 2021; 5:e2100773. [PMID: 34310085 DOI: 10.1002/adbi.202100773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/19/2021] [Indexed: 12/22/2022]
Abstract
Nitrite and nitric oxide (NO) are two active nitrogen oxides that display similar biochemical properties, especially when interacting with redox-sensitive proteins (i.e., hemoproteins), an observation serving as the foundation of the notion that the antibacterial effect of nitrite is largely attributed to NO formation. However, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. Although both nitrite and NO are formed and decomposed by enzymes participating in the transformation of these nitrogen species, NO can also be generated via amino acid metabolism by bacterial NO synthetase and scavenged by flavohemoglobin. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to heme-copper oxidases. Consequently, the homeostasis of redox-sensitive proteins may be responsible for the substantial difference in NO-targets identified to date among different bacteria. In addition, most protective systems against NO damage have no significant role in alleviating inhibitory effects of nitrite. Furthermore, when functioning as signal molecules, nitrite and NO are perceived by completely different sensing systems, through which they are linked to different biological processes.
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Affiliation(s)
- Kailun Guo
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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22
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Yi YC, Ng IS. Redirection of metabolic flux in Shewanella oneidensis MR-1 by CRISPRi and modular design for 5-aminolevulinic acid production. BIORESOUR BIOPROCESS 2021; 8:13. [PMID: 38650245 PMCID: PMC10992681 DOI: 10.1186/s40643-021-00366-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/01/2021] [Indexed: 11/10/2022] Open
Abstract
Programming non-canonical organisms is more attractive due to the prospect of high-value chemical production. Among all, Shewanella oneidensis MR-1 possesses outstanding heme synthesis ability and is well-known for electron transfer, thus has high potential in microbial fuel cell and bioremediation. However, heme, as the final product of C4 and C5 pathways, is regulated by heme cluster for the high-value 5-aminolevulinic acid (ALA) for cancer photodynamic therapy, which has never been explored in MR-1. Herein, the heme metabolism in MR-1 was firstly optimized for ALA production. We applied CRISPR interference (CRISPRi) targeted on the genes to fine-tune carbon flux in TCA cycle and redirected the carbon out-flux from heme, leading to a significant change in the amino acid profiles, while downregulation of the essential hemB showed a 2-fold increasing ALA production via the C5 pathway. In contrast, the modular design including of glucokinase, GroELS chaperone, and ALA synthase from Rhodobacter capsulatus enhanced ALA production markedly in the C4 pathway. By integrating gene cluster under dual T7 promoters, we obtained a new strain M::TRG, which significantly improved ALA production by 145-fold. We rewired the metabolic flux of MR-1 through this modular design and successfully produced the high-value ALA compound at the first time.
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Affiliation(s)
- Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
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23
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Liu L, Feng X, Wang W, Chen Y, Chen Z, Gao H. Free Rather Than Total Iron Content Is Critically Linked to the Fur Physiology in Shewanella oneidensis. Front Microbiol 2020; 11:593246. [PMID: 33329474 PMCID: PMC7732582 DOI: 10.3389/fmicb.2020.593246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/29/2020] [Indexed: 11/30/2022] Open
Abstract
Ferric uptake regulator (Fur) is a transcriptional regulator playing a central role in iron homeostasis of many bacteria, and Fur inactivation commonly results in pleiotropic phenotypes. In Shewanella oneidensis, a representative of dissimilatory metal-reducing γ-proteobacteria capable of respiring a variety of chemicals as electron acceptors (EAs), Fur loss substantially impairs respiration. However, to date the mechanism underlying the physiological phenomenon remains obscure. This investigation reveals that Fur loss compromises activity of iron proteins requiring biosynthetic processes for their iron cofactors, heme in particular. We then show that S. oneidensis Fur is critical for maintaining heme homeostasis by affecting both its biosynthesis and decomposition of the molecule. Intriguingly, the abundance of iron-containing proteins controlled by H2O2-responding regulator OxyR increases in the fur mutant because the Fur loss activates OxyR. By comparing suppression of membrane-impermeable, membrane-permeable, and intracellular-only iron chelators on heme deficiency and elevated H2O2 resistance, our data suggest that the elevation of the free iron content by the Fur loss is likely to be the predominant factor for the Fur physiology. Overall, these results provide circumstantial evidence that Fur inactivation disturbs bacterial iron homeostasis by altering transcription of its regulon members, through which many physiological processes, such as respiration and oxidative stress response, are transformed.
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Affiliation(s)
| | | | | | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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24
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Ng CK, Xu J, Cai Z, Yang L, Thompson IP, Huang WE, Cao B. Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes. Microb Biotechnol 2020; 13:1904-1916. [PMID: 32729223 PMCID: PMC7533324 DOI: 10.1111/1751-7915.13636] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/03/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Electrochemically active biofilms are capable of exchanging electrons with solid electron acceptors and have many energy and environmental applications such as bioelectricity generation and environmental remediation. The performance of electrochemically active biofilms is usually dependent on c-type cytochromes, while biofilm development is controlled by a signal cascade mediated by the intracellular secondary messenger bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP). However, it is unclear whether there are any links between the c-di-GMP regulatory system and the expression of c-type cytochromes. In this study, we constructed a S. oneidensis MR-1 strain with a higher cytoplasmic c-di-GMP level by constitutively expressing a c-di-GMP synthase and it exhibited expected c-di-GMP-influenced traits, such as lowered motility and increased biofilm formation. Compared to MR-1 wild-type strain, the high c-di-GMP strain had a higher Fe(III) reduction rate (21.58 vs 11.88 pM of Fe(III)/h cell) and greater expression of genes that code for the proteins involved in the Mtr pathway, including CymA, MtrA, MtrB, MtrC and OmcA. Furthermore, single-cell Raman microspectroscopy (SCRM) revealed a great increase of c-type cytochromes in the high c-di-GMP strain as compared to MR-1 wild-type strain. Our results reveal for the first time that the c-di-GMP regulation system indirectly or directly positively regulates the expression of cytochromes involved in the extracellular electron transport (EET) in S. oneidensis, which would help to understand the regulatory mechanism of c-di-GMP on electricity production in bacteria.
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Affiliation(s)
- Chun Kiat Ng
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore City, Singapore
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25
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Su L, Fukushima T, Ajo-Franklin CM. A hybrid cyt c maturation system enhances the bioelectrical performance of engineered Escherichia coli by improving the rate-limiting step. Biosens Bioelectron 2020; 165:112312. [PMID: 32729471 DOI: 10.1016/j.bios.2020.112312] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Bioelectronic devices can use electron flux to enable communication between biotic components and abiotic electrodes. We have modified Escherichia coli to electrically interact with electrodes by expressing the cytochrome c from Shewanella oneidensis MR-1. However, we observe inefficient electrical performance, which we hypothesize is due to the limited compatibility of the E. coli cytochrome c maturation (Ccm) systems with MR-1 cytochrome c. Here we test whether the bioelectronic performance of E. coli can be improved by constructing hybrid Ccm systems containing protein domains from both E. coli and S. oneidensis MR-1. The hybrid CcmH increased cytochrome c expression by increasing the abundance of CymA 60%, while only slightly changing the abundance of the other cytochromes c. Electrochemical measurements showed that the overall current from the hybrid ccm strain increased 121% relative to the wildtype ccm strain, with an electron flux per cell of 12.3 ± 0.3 fA·cell-1. Additionally, the hybrid ccm strain doubled its electrical response with the addition of exogenous flavin, and quantitative analysis of this demonstrates CymA is the rate-limiting step in this electron conduit. These results demonstrate that this hybrid Ccm system can enhance the bioelectrical performance of the cyt c expressing E. coli, allowing the construction of more efficient bioelectronic devices.
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Affiliation(s)
- Lin Su
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210018, China; Department of BioSciences, Rice University, Houston, TX, 77005, USA; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tatsuya Fukushima
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Caroline M Ajo-Franklin
- Department of BioSciences, Rice University, Houston, TX, 77005, USA; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Molecular Biophysics and Integrated Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Biosciences and Bioengineering, Rice University, Houston, TX, 77005, USA.
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26
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Liang H, Zhang Y, Wang S, Gao H. Mutual interplay between ArcA and σ E orchestrates envelope stress response in Shewanella oneidensis. Environ Microbiol 2020; 23:652-668. [PMID: 32372525 DOI: 10.1111/1462-2920.15060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/03/2020] [Indexed: 01/15/2023]
Abstract
To survive and thrive in harsh and ever-changing environments, intricate mechanisms have evolved for bacterial cells to monitor perturbations impacting the integrity of their envelope and to mount an appropriate response to contain or repair the damage. In this study, we report in Shewanella oneidensis a previously undescribed mechanism for the envelope defect resulting from the loss of Arc, a two-component transcriptional regulatory system crucial for respiration. We uncovered σE , a master regulator establishing and maintaining the integrity of the cell envelope in γ-proteobacteria, as the determining factor for the cell envelope defect of the arcA mutant. When ArcA is depleted, σE activity is compromised by enhanced production of anti-σE protein RseA. Surprisingly, S. oneidensis σE is not essential for viability, but becomes so in the absence of ArcA. Furthermore, we demonstrated that there is an interplay between these two regulators as arcA expression is affected by availability of σE . Overall, our results underscore functional interplay of regulatory systems for envelope stress response: although each of the systems may respond to perturbation of particular components of the envelope, they are functionally intertwined, working together to form an interconnected safety net.
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Affiliation(s)
- Huihui Liang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Yongting Zhang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Sijing Wang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
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27
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28
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Li J, Tang Q, Li Y, Fan YY, Li FH, Wu JH, Min D, Li WW, Lam PKS, Yu HQ. Rediverting Electron Flux with an Engineered CRISPR-ddAsCpf1 System to Enhance the Pollutant Degradation Capacity of Shewanella oneidensis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3599-3608. [PMID: 32062962 DOI: 10.1021/acs.est.9b06378] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pursuing efficient approaches to promote the extracellular electron transfer (EET) of extracellular respiratory bacteria is essential to their application in environmental remediation and waste treatment. Here, we report a new strategy of tuning electron flux by clustered regularly interspaced short palindromic repeat (CRISPR)-ddAsCpf1-based rediverting (namely STAR) to enhance the EET capacity of Shewanella oneidensis MR-1, a model extracellular respiratory bacterium widely present in the environment. The developed CRISPR-ddAsCpf1 system enabled approximately 100% gene repression with the green fluorescent protein (GFP) as a reporter. Using a WO3 probe, 10 representative genes encoding for putative competitive electron transfer proteins were screened, among which 7 genes were identified as valid targets for EET enhancement. Repressing the valid genes not only increased the transcription level of the l-lactate metabolism genes but also affected the genes involved in direct and indirect EET. Increased riboflavin production was also observed. The feasibility of this strategy to enhance the bioreduction of methyl orange, an organic pollutant, and chromium, a typical heavy metal, was demonstrated. This work implies a great potential of the STAR strategy with the CIRPSR-ddAsCpf1 system for enhancing bacterial EET to favor more efficient environmental remediation applications.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, 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 215123, China
- State Key Laboratory in Marine Pollution, Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong SAR, China
| | - Qiang Tang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yang Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yang-Yang Fan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Feng-He Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Jing-Hang Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, 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 215123, China
| | - Paul K S Lam
- University of Science and Technology of China-City University of Hong Kong Joint Advanced Research Center, Suzhou 215123, China
- State Key Laboratory in Marine Pollution, Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong SAR, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, 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 215123, China
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29
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Kong G, Song D, Guo J, Sun G, Zhu C, Chen F, Yang Y, Xu M. Lack of Periplasmic Non-heme Protein SorA Increases Shewanella decolorationis Current Generation. Front Microbiol 2020; 11:262. [PMID: 32158435 PMCID: PMC7052111 DOI: 10.3389/fmicb.2020.00262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 02/04/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial extracellular electron transport (EET) plays an important role in many natural and engineering processes. Some periplasmic non-heme redox proteins usually coexist with c-type cytochromes (CTCs) during the EET process. However, in contrast to CTCs, little is known about the roles of these non-heme redox proteins in EET. In this study, the transcriptome of Shewanella decolorationis S12 showed that the gene encoding a periplasmic sulfite dehydrogenase molybdenum-binding subunit SorA was significantly up-regulated during electrode respiration in microbial fuel cells (MFCs) compared with that during azo-dye reduction. The maximum current density of MFCs catalyzed by a mutant strain lacking SorA (ΔsorA) was 25% higher than that of wild strain S12 (20 vs. 16 μA/cm2). Both biofilm formation and the current generation of the anodic biofilms were increased by the disruption of sorA, which suggests that the existence of SorA in S. decolorationis S12 inhibits electrode respiration. In contrast, disruption of sorA had no effect on respiration by S. decolorationis S12 with oxygen, fumarate, azo dye, or ferric citrate as electron acceptors. This is the first report of the specific effect of a periplasmic non-heme redox protein on EET to electrode and provides novel information for enhancing bacterial current generation.
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Affiliation(s)
- Guannan Kong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Da Song
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jun Guo
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Guoping Sun
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chunjie Zhu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fusheng Chen
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yonggang Yang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China
| | - Meiying Xu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
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30
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Basu A, Wanner C, Johnson TM, Lundstrom CC, Sanford RA, Sonnenthal EL, Boyanov MI, Kemner KM. Microbial U Isotope Fractionation Depends on the U(VI) Reduction Rate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2295-2303. [PMID: 31909614 DOI: 10.1021/acs.est.9b05935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
U isotope fractionation may serve as an accurate proxy for U(VI) reduction in both modern and ancient environments, if the systematic controls on the magnitude of fractionation (ε) are known. We model the effect of U(VI) reduction kinetics on U isotopic fractionation during U(VI) reduction by a novel Shewanella isolate, Shewanella sp. (NR), in batch incubations. The measured ε values range from 0.96 ± 0.16 to 0.36 ± 0.07‰ and are strongly dependent on the U(VI) reduction rate. The ε decreases with increasing reduction rate constants normalized by cell density and initial U(VI). Reactive transport simulations suggest that the rate dependence of ε is due to a two-step process, where diffusive transport of U(VI) from the bulk solution across a boundary layer is followed by enzymatic reduction. Our results imply that the spatial decoupling of bulk U(VI) solution and enzymatic reduction should be taken into account for interpreting U isotope data from the environment.
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Affiliation(s)
- Anirban Basu
- Department of Earth Sciences, Royal Holloway , University of London , Egham TW20 0EX , U.K
| | - Christoph Wanner
- Institute of Geological Sciences , University of Bern , Baltzerstrasse 3 , Bern CH-3012 , Switzerland
| | - Thomas M Johnson
- Department of Geology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Craig C Lundstrom
- Department of Geology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Robert A Sanford
- Department of Geology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Eric L Sonnenthal
- Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Maxim I Boyanov
- Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
- Institute of Chemical Engineering , Bulgarian Academy of Sciences , Sofia 1113 , Bulgaria
| | - Kenneth M Kemner
- Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
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Regulation and Maturation of the Shewanella oneidensis Sulfite Reductase SirA. Sci Rep 2020; 10:953. [PMID: 31969587 PMCID: PMC6976685 DOI: 10.1038/s41598-020-57587-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/27/2019] [Indexed: 01/12/2023] Open
Abstract
Shewanella oneidensis, a metal reducer and facultative anaerobe, expresses a large number of c-type cytochromes, many of which function as anaerobic reductases. All of these proteins contain the typical heme-binding motif CXXCH and require the Ccm proteins for maturation. Two c-type cytochrome reductases also possess atypical heme-binding sites, the NrfA nitrite reductase (CXXCK) and the SirA sulfite reductase (CX12NKGCH). S. oneidensis MR-1 encodes two cytochrome c synthetases (CcmF and SirE) and two apocytochrome c chaperones (CcmI and SirG). SirE located in the sir gene cluster is required for the maturation of SirA, but not NrfA. Here we show that maturation of SirA requires the combined function of the two apocytochrome c chaperones CcmI and SirG. Loss of either protein resulted in decreased sulfite reductase. Furthermore, SirA was not detected in a mutant that lacked both chaperones, perhaps due to misfolding or instability. These results suggest that CcmI interacts with SirEFG during SirA maturation, and with CcmF during maturation of NrfA. Additionally, we show that CRP regulates expression of sirA via the newly identified transcriptional regulatory protein, SirR.
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32
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Su L, Fukushima T, Prior A, Baruch M, Zajdel TJ, Ajo-Franklin CM. Modifying Cytochrome c Maturation Can Increase the Bioelectronic Performance of Engineered Escherichia coli. ACS Synth Biol 2020; 9:115-124. [PMID: 31880923 DOI: 10.1021/acssynbio.9b00379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genetic circuits that encode extracellular electron transfer (EET) pathways allow the intracellular state of Escherichia coli to be electronically monitored and controlled. However, relatively low electron flux flows through these pathways, limiting the degree of control by these circuits. Since the EET pathway is composed of multiple multiheme cytochromes c (cyts c) from Shewanella oneidensis MR-1, we hypothesized that lower expression levels of cyt c may explain this low EET flux and may be caused by the differences in the cyt c maturation (ccm) machinery between these two species. Here, we constructed random mutations within ccmH by error-prone PCR and screened for increased cyt c production. We identified two ccmH mutants, ccmH-132 and ccmH-195, that exhibited increased heterologous cyt c expression, but had different effects on EET. The ccmH-132 strain reduced WO3 nanoparticles faster than the parental control, whereas the ccmH-195 strain reduced more slowly. The same trend is reflected in electrical current generation: ccmH-132, which has only a single mutation from WT, drastically increased current production by 77%. The percentage of different cyt c proteins in these two mutants suggests that the stoichiometry of the S. oneidensis cyts c is a key determinant of current production by Mtr-expressing E. coli. Thus, we conclude that modulating cyt c maturation effectively improves genetic circuits governing EET in engineered biological systems, enabling better bioelectronic control of E. coli.
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Affiliation(s)
- Lin Su
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210018, China
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tatsuya Fukushima
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew Prior
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Moshe Baruch
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tom J. Zajdel
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Caroline M. Ajo-Franklin
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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33
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Wu G, Jin F. Pellicle development of Shewanella oneidensis is an aerotaxis-piloted and energy-dependent process. Biochem Biophys Res Commun 2019; 519:127-133. [PMID: 31481239 DOI: 10.1016/j.bbrc.2019.08.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/26/2019] [Indexed: 11/19/2022]
Abstract
Pellicles are biofilms found at the air-liquid interface and are widely distributed in natural environments. In this study, a simple pellicle detection method was established, and using this new method, the pellicle formation activities of Shewanella oneidensis MR-1 and its 42 cytochrome c mutants were analysed. The results showed that the pellicle was initiated at very early stages of incubation. Aerotaxis was the major external factor, while energy acquirement was the main internal factor for pellicle initiation. Among the 42 cytochrome c mutants, 17 mutants, including those deficient in aerobic respiration, sulfur or sulfite/sulfate respiration, nitrite respiration, metal respiration, DMSO respiration and fumarate respiration, exhibited delayed pellicle initiation. The results suggest that S. oneidensis utilizes the electron acceptors simultaneously under anoxic conditions and that the disruption of any of these anaerobic respiration routes would retard pellicle initiation.
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Affiliation(s)
- Genfu Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Feifei Jin
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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34
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Distinct Roles of Shewanella oneidensis Thioredoxin in Regulation of Cellular Responses to Hydrogen and Organic Peroxides. Appl Environ Microbiol 2019; 85:AEM.01700-19. [PMID: 31444207 DOI: 10.1128/aem.01700-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022] Open
Abstract
The thioredoxin (Trx) and glutaredoxin (Grx) antioxidant systems are deeply involved in bacterial response to oxidative stress, but to date, we know surprisingly little about the roles of these systems in response to reactive oxygen species (ROS) other than hydrogen peroxide (H2O2). In this study, we used Shewanella oneidensis, an environmental bacterium, as a research model to investigate the roles of Trx and Grx in oxidative stress response because it has functionally intertwined ROS responsive regulators OxyR and OhrR. We found that Trx1 is the major thiol/disulfide redox system and that in its absence a Grx system becomes essential under normal conditions. Although overshadowed by Trx1 in the wild type, Trx2 can fully replace Trx1 in physiology when overproduced. Trx1 is required for OxyR to function as a repressor but, more importantly, plays a critical role in the cellular response to organic peroxide (OP) by mediating the redox status of OhrR but not OP scavenger OhrA. While none of the trx and grx genes are OxyR dependent, trxA and trxC are affected by OhrR indirectly. Additional data suggest that depletion of glutathione is likely the cue to trigger induced expression of trxA and trxC These findings underscore the particular importance of Trx in the bacterial OP stress response.IMPORTANCE The Trx and Grx systems are deeply involved in bacterial responses to H2O2-induced oxidative stress. However, little is known about their roles in response to other ROS, such as organic peroxides (OPs). In this study, we used S. oneidensis as a research model to investigate the interplay between Trx/Grx and OxyR/OhrR. We show that Trxs mediate the redox status of transcriptional OP-responding regulator OhrR. Although none of the trx or grx genes are directly controlled by OxyR or OhrR, expression of trxA and trxC is induced by tert-butyl hydroperoxide (t-BHP). We further show that the trxA and trxC genes respond to effects of glutathione (GSH) depletion rather than oxidation. These findings underscore the particular importance of Trx in the bacterial OP stress response.
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Improvement of the electron transfer rate in Shewanella oneidensis MR-1 using a tailored periplasmic protein composition. Bioelectrochemistry 2019; 129:18-25. [PMID: 31075535 DOI: 10.1016/j.bioelechem.2019.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 04/28/2019] [Accepted: 04/28/2019] [Indexed: 11/23/2022]
Abstract
Periplasmic c-type cytochromes are essential for the electron transport between the cytoplasmic membrane bound menquinol oxidase CymA and the terminal ferric iron reductase MtrABC in the outer membrane of Shewanella oneidensis cells. Either STC or FccA are necessary for periplasmic electron transfer. We followed the hypothesis that the elimination of potential competing reactions in the periplasm and the simultaneous overexpression of STC (cctA) could lead to an accelerated electron transfer to the cell surface. The genes nrfA, ccpA, napB and napA were replaced by cctA. This led to a 1.7-fold increased ferric iron reduction rate and a 23% higher current generation in a bioelectrochemical system. Moreover, the quadruple mutant had a higher periplasmic flavin content. Further deletion of fccA and its replacement by cctA resulted in a strain with ferric iron reduction rates similar to the wild type and a lower concentration of periplasmic flavin compared to the quadruple mutant. A transcriptomic analysis revealed that the quadruple mutant had a 3.7-fold higher cctA expression which could not be further increased by the replacement of fccA. This work indicates that a synthetic adaptation of Shewanella towards extracellular respiration holds potential for increased respiratory rates and consequently higher current densities.
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36
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DING DEWU. NETWORK ANALYSIS OF COMMON DIFFERENTIAL GENES IDENTIFIES KEY GENES AND IMPORTANT MODULES UNDERLYING EXTRACELLULAR ELECTRON TRANSFER PROCESSES. J BIOL SYST 2019. [DOI: 10.1142/s0218339019500037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electricigens can transfer electrons that produced in intracellular metabolic processes to cellular surface to restore extracellular insoluble electron acceptors (extracellular electron transfer, EET). To uncover the molecular mechanisms underlying EET processes, we integrated transcriptome changes accompanying such processes with molecular network. Firstly, time-series expression datasets for Shewanella oneidensis MR-1 under limited/changed [Formula: see text] conditions were obtained from the GEO database, and a total of 336 common differentially expressed genes (DEGs) were identified. Then, we constructed the protein–protein interaction (PPI) network that involved in EET processes from these DEGs. Furthermore, by using centralization analysis and community detection, network analysis of the PPI network was performed. Although the fundamental EET genes are similar to previous studies, important new genes have been discovered. Taking together, our study identified many literature-validated genes critical to EET processes, and also proposed some novel genes that were putatively involved in EET processes.
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Affiliation(s)
- DEWU DING
- School of Mathematics and Computer Science, Yichun University, Yichun 336000, P. R. China
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37
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Michelson K, Alcalde RE, Sanford RA, Valocchi AJ, Werth CJ. Diffusion-Based Recycling of Flavins Allows Shewanella oneidensis MR-1 To Yield Energy from Metal Reduction Across Physical Separations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3480-3487. [PMID: 30840821 DOI: 10.1021/acs.est.8b04718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We fabricated a microfluidic reactor with a nanoporous barrier to characterize electron transport between Shewanella oneidensis MR-1 and the metal oxide birnessite across a physical separation. Real-time quantification of electron flux across this barrier by strains with different electron transfer capabilities revealed that this bacterium exports flavins to its surroundings when faced with no direct physical access to an electron acceptor, allowing it to reduce metals at distances exceeding 60 μm. An energy balance indicates that flavins must be recycled for S. oneidensis MR-1 to yield energy from lactate oxidation coupled to flavin reduction. In our system, we find that flavins are recycled between 24 and 60 times depending on flow conditions. This energy saving strategy, which until now had not been systematically tested or captured in environmentally relevant systems, suggests that electron shuttling microorganisms have the capacity to access and reduce metals in physically distant or potentially toxic microenvironments (i.e., pores with soluble and transiently sorbed toxins) where direct contact is limited or unfavorable. Our results challenge the prediction that diffusion-based electron shuttling is only effective across short distances and may lead to improved bioremediation strategies or advance biogeochemical models of electron transfer in anaerobic sediments.
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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 East Dean Keeton Street , Austin , Texas 78712 , United States
| | - Reinaldo E Alcalde
- Department of Civil, Architectural, and Environmental Engineering , University of Texas at Austin , 301 East Dean Keeton Street , Austin , Texas 78712 , United States
| | - Robert A Sanford
- Department of Geology , University of Illinois at Urbana-Champaign , 605 East Springfield Avenue , Champaign , Illinois 61820 , 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 East Dean Keeton Street , Austin , Texas 78712 , United States
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38
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Cytochromes c Constitute a Layer of Protection against Nitric Oxide but Not Nitrite. Appl Environ Microbiol 2018; 84:AEM.01255-18. [PMID: 29934335 DOI: 10.1128/aem.01255-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/20/2018] [Indexed: 11/20/2022] Open
Abstract
Nitric oxide (NO) is a radical gas that reacts with various biological molecules in complex ways to inhibit growth as a bacteriostatic agent. NO is nearly ubiquitous because it can be generated both biotically and abiotically. To protect the cell from NO damage, bacteria have evolved many strategies, with the production of detoxifying enzymatic systems being the most efficient. Here, we report that c-type cytochromes (cytochromes c) constitute a primary NO protection system in Shewanella oneidensis, a Gram-negative environmental bacterium renowned for respiratory versatility due to its high cytochrome c content. By using mutants producing cytochromes c at varying levels, we found that the content of these proteins is inversely correlated with the growth inhibition imposed by NO, whereas the effect of each individual cytochrome c is negligible. This NO-protecting system has no effect on nitrite inhibition. In the absence of cytochromes c, other NO targets and protective proteins, such as NnrS, emerge to show physiological influences during the NO stress. We further demonstrate that cytochromes c also play a similar role in Escherichia coli, albeit only modestly. Our data thus identify the in vivo function of an important group of proteins in alleviating NO stress.IMPORTANCE It is widely accepted that the antibacterial effects of nitrite are attributable to nitric oxide (NO) formation, suggesting a correlation of bacterial susceptibilities to these two chemicals. However, compared to E. coli, S. oneidensis is highly sensitive to nitrite but resistant to NO, implying the presence of robust NO-protective systems. Here, we show that c-type cytochromes (cytochromes c) play a main role in protecting S. oneidensis against damages from NO but not from nitrite. In their absence, impacts of proteins that promote NO tolerance and that are targets of NO inhibition become evident. Our data thus reveal the specific activity of cytochromes c in alleviating the stress caused by NO but not nitrite.
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Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J. Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Mol Microbiol 2018; 109:571-583. [PMID: 29995975 DOI: 10.1111/mmi.14067] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach the cell surface and what the minimal set of electron transport proteins to the cell surface is. Nevertheless, even after decades of work in different research groups around the globe there are still several important questions that were not answered yet. In particular, the physiology of this organism, the possible evolutionary benefit of some responses to anoxic conditions, as well as the exact mechanism of electron transfer onto solid electron acceptors are yet to be addressed. The elucidation of these questions will be a great challenge for future work and important for the application of extracellular respiration in biotechnological processes.
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Affiliation(s)
- Sebastian Beblawy
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Thea Bursac
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Catarina Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Ricardo Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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Distinct Nitrite and Nitric Oxide Physiologies in Escherichia coli and Shewanella oneidensis. Appl Environ Microbiol 2018; 84:AEM.00559-18. [PMID: 29654177 DOI: 10.1128/aem.00559-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/06/2018] [Indexed: 11/20/2022] Open
Abstract
Nitrite has been used as a bacteriostatic agent for centuries in food preservation. It is widely accepted that this biologically inert molecule functions indirectly, serving as a stable reservoir of bioactive nitric oxide (NO) and other reactive nitrogen species to impact physiology. As a result, to date, we know surprisingly little about in vivo targets of nitrite. Here, we carry out comparative analyses of nitrite and NO physiology in Escherichia coli and in Shewanella oneidensis, a Gram-negative environmental bacterium renowned for respiratory versatility. These two bacteria differ from each other in many aspects of nitrite and NO physiology, including NO generation, NO degradation, and unexpectedly, their contrary susceptibility to nitrite and NO. In cell extracts of both bacteria, most of the NO targets are also susceptible to nitrite, and vice versa. However, with respect to growth inhibition caused by NO, the targets are impacted distinctly; NO targets are responsible for the inhibition of growth of E. coli but not of S. oneidensis More surprisingly, all proteins identified to be implicated in NO tolerance in other bacteria appear to play a dispensable role in protecting S. oneidensis against NO. These data suggest that S. oneidensis is equipped with a robust but yet unknown NO protecting system. In the case of nitrite, it is clear that the target of physiological significance in both bacteria is cytochrome heme-copper oxidase.IMPORTANCE Nitrite is toxic to living organisms at high levels, but such antibacterial effects of nitrite are attributable to the formation of nitric oxide (NO), a highly reactive radical gas molecule. Here, we report that Shewanella oneidensis is highly resistant to NO but sensitive to nitrite compared to Escherichia coli by approximately 4-fold. In both bacteria, nitrite inhibits bacterial growth by targeting cytochrome heme-copper oxidase. In contrast, the targets of NO are diverse. Although these targets are similar in E. coli and S. oneidensis, they are responsible for growth inhibition caused by NO in the former but not in the latter. Overall, the presented data, along with the previous data, solidify a proposal that the in vivo targets of NO and nitrite in bacteria are largely different.
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Shewanella oneidensis as a living electrode for controlled radical polymerization. Proc Natl Acad Sci U S A 2018; 115:4559-4564. [PMID: 29666254 DOI: 10.1073/pnas.1800869115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolic engineering has facilitated the production of pharmaceuticals, fuels, and soft materials but is generally limited to optimizing well-defined metabolic pathways. We hypothesized that the reaction space available to metabolic engineering could be expanded by coupling extracellular electron transfer to the performance of an exogenous redox-active metal catalyst. Here we demonstrate that the electroactive bacterium Shewanella oneidensis can control the activity of a copper catalyst in atom-transfer radical polymerization (ATRP) via extracellular electron transfer. Using S. oneidensis, we achieved precise control over the molecular weight and polydispersity of a bioorthogonal polymer while similar organisms, such as Escherichia coli, showed no significant activity. We found that catalyst performance was a strong function of bacterial metabolism and specific electron transport proteins, both of which offer potential biological targets for future applications. Overall, our results suggest that manipulating extracellular electron transport pathways may be a general strategy for incorporating organometallic catalysis into the repertoire of metabolically controlled transformations.
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Meibom KL, Cabello EM, Bernier-Latmani R. The Small RNA RyhB Is a Regulator of Cytochrome Expression in Shewanella oneidensis. Front Microbiol 2018. [PMID: 29515549 PMCID: PMC5826389 DOI: 10.3389/fmicb.2018.00268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Shewanella oneidensis produces an extensive electron transfer network that results in metabolic flexibility. A large number of c-type cytochromes are expressed by S. oneidensis and these function as the fundamental electron transport chain proteins. Although several S. oneidensis cytochromes have been well-characterized, little is known about how their expression is regulated. In this study, we investigate the role of the ferric uptake regulator (Fur) and the sRNA RyhB in regulation. Our results demonstrate that loss of Fur leads to diminished growth and an apparent decrease in heme-containing proteins. Remarkably, deleting the Fur-repressed ryhB gene almost completely reverses these physiological changes, indicating that the phenotypes resulting from loss of Fur are (at least partially) dependent on RyhB. RNA sequencing identified a number of possible RyhB repressed genes. A large fraction of these encode c-type cytochromes, among them two of the most abundant periplasmic cytochromes CctA (also known as STC) and ScyA. We show that RyhB destabilizes the mRNA of four of its target genes, cctA, scyA, omp35, and nrfA and this requires the presence of the RNA chaperone Hfq. Iron limitation decreases the expression of the RyhB target genes cctA and scyA and this regulation relies on the presence of both Fur and RyhB. Overall, this study suggests that controlling cytochrome expression is of importance to maintain iron homeostasis and that sRNAs molecules are important players in the regulation of fundamental processes in S. oneidensis MR-1.
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Affiliation(s)
- Karin L Meibom
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elena M Cabello
- Bioinformatics and Biostatistics Core Facility, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Effect of the anode potential on the physiology and proteome of Shewanella oneidensis MR-1. Bioelectrochemistry 2018; 119:172-179. [DOI: 10.1016/j.bioelechem.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 11/19/2022]
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Harris HW, Sánchez-Andrea I, McLean JS, Salas EC, Tran W, El-Naggar MY, Nealson KH. Redox Sensing within the Genus Shewanella. Front Microbiol 2018; 8:2568. [PMID: 29422884 PMCID: PMC5789149 DOI: 10.3389/fmicb.2017.02568] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/11/2017] [Indexed: 11/28/2022] Open
Abstract
A novel bacterial behavior called congregation was recently described in Shewanella oneidensis MR-1 as the accumulation of cells around insoluble electron acceptors (IEA). It is the result of a series of "run-and-reversal" events enabled by modulation of swimming speed and direction. The model proposed that the swimming cells constantly sense their surroundings with specialized outer membrane cytochromes capable of extracellular electron transport (EET). Up to this point, neither the congregation nor attachment behavior have been studied in any other strains. In this study, the wild type of S. oneidensis MR-1 and several deletion mutants as well as eight other Shewanella strains (Shewanella putrefaciens CN32, S. sp. ANA-3, S. sp. W3-18-1, Shewanella amazonensis SB2B, Shewanella loihica PV-4, Shewanella denitrificans OS217, Shewanella baltica OS155, and Shewanella frigidimarina NCIMB400) were screened for the ability to congregate. To monitor congregation and attachment, specialized cell-tracking techniques, as well as a novel cell accumulation after photo-bleaching (CAAP) confocal microscopy technique were utilized in this study. We found a strong correlation between the ability of strain MR-1 to accumulate on mineral surface and the presence of key EET genes such as mtrBC/omcA (SO_1778, SO_1776, and SO_1779) and gene coding for methyl-accepting protein (MCPs) with Ca+ channel chemotaxis receptor (Cache) domain (SO_2240). These EET and taxis genes were previously identified as essential for characteristic run and reversal swimming around IEA surfaces. CN32, ANA-3, and PV-4 congregated around both Fe(OH)3 and MnO2. Two other Shewanella spp. showed preferences for one oxide over the other: preferences that correlated with the metal content of the environments from which the strains were isolated: e.g., W3-18-1, which was isolated from an iron-rich habitat congregated and attached preferentially to Fe(OH)3, while SB2B, which was isolated from a MnO2-rich environment, preferred MnO2.
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Affiliation(s)
- Howard W. Harris
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | | | - Jeffrey S. McLean
- Department of Periodontics, University of Washington, Seattle, WA, United States
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States
| | | | - William Tran
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | - Mohamed Y. El-Naggar
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, Biological Sciences and Physics, University of Southern California, Los Angeles, CA, United States
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Yilmazel YD, Zhu X, Kim KY, Holmes DE, Logan BE. Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari. Bioelectrochemistry 2017; 119:142-149. [PMID: 28992595 DOI: 10.1016/j.bioelechem.2017.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 02/07/2023]
Abstract
Few microorganisms have been examined for current generation under thermophilic (40-65°C) or hyperthermophilic temperatures (≥80°C) in microbial electrochemical systems. Two iron-reducing archaea from the family Archaeoglobaceae, Ferroglobus placidus and Geoglobus ahangari, showed electro-active behavior leading to current generation at hyperthermophilic temperatures in single-chamber microbial electrolysis cells (MECs). A current density (j) of 0.68±0.11A/m2 was attained in F. placidus MECs at 85°C, and 0.57±0.10A/m2 in G. ahangari MECs at 80°C, with an applied voltage of 0.7V. Cyclic voltammetry (CV) showed that both strains produced a sigmoidal catalytic wave, with a mid-point potential of -0.39V (vs. Ag/AgCl) for F. placidus and -0.37V for G. ahangari. The comparison of CVs using spent medium and turnover CVs, coupled with the detection of peaks at the same potentials in both turnover and non-turnover conditions, suggested that mediators were not used for electron transfer and that both archaea produced current through direct contact with the electrode. These two archaeal species, and other hyperthermophilic exoelectrogens, have the potential to broaden the applications of microbial electrochemical technologies for producing biofuels and other bioelectrochemical products under extreme environmental conditions.
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Affiliation(s)
- Yasemin D Yilmazel
- Department of Chemical Engineering, Rochester Institute of Technology, Rochester, NY, USA; Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
| | - Xiuping Zhu
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Kyoung-Yeol Kim
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Dawn E Holmes
- Department of Biology, Western New England University, Springfield, MA, USA
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA
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Dong Z, Guo S, Fu H, Gao H. Investigation of a spontaneous mutant reveals novel features of iron uptake in Shewanella oneidensis. Sci Rep 2017; 7:11788. [PMID: 28924168 PMCID: PMC5603553 DOI: 10.1038/s41598-017-11987-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/30/2017] [Indexed: 12/03/2022] Open
Abstract
Shewanella oneidensis is among the first and the best studied bacteria capable of respiring minerals as terminal electron acceptors (EAs), including a variety of iron ores. This respiration process relies on a large number of c-type cytochromes, which per se are iron-containing proteins. Thus, iron plays an essential and special role in iron respiration of S. oneidensis, prompting extensive investigations into iron physiology. Despite this, we still know surprisingly little about the components and characteristics of iron transport in this bacterium. Here, we report that TonB-dependent receptor PutA (SO_3033) is specific to the siderophore-mediated iron uptake. Although homologs of PutA are abundant, none of them can function as a replacement. In the absence of PutA, S. oneidensis suffers from an iron shortage, which leads to a severe defect in production of cytochrome c. However, proteins requiring other types of cytochromes, such as b and d, do not appear to be significantly impacted. Intriguingly, lactate, but not other carbon sources that are routinely used to support growth, is able to promote iron uptake when PutA is missing. We further show that the lactate-mediated iron import is independent of lactate permeases. Overall, our results suggest that in S. oneidensis the siderophore-dependent pathway plays a key role in iron uptake when iron is limited, but many alternative routes exist.
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Affiliation(s)
- Ziyang Dong
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shupan Guo
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Huihui Fu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors. PLoS One 2017; 12:e0184994. [PMID: 28915277 PMCID: PMC5600388 DOI: 10.1371/journal.pone.0184994] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/04/2017] [Indexed: 02/08/2023] Open
Abstract
Current technologies are lacking in the area of deployable, in situ monitoring of complex chemicals in environmental applications. Microorganisms metabolize various chemical compounds and can be engineered to be analyte-specific making them naturally suited for robust chemical sensing. However, current electrochemical microbial biosensors use large and expensive electrochemistry equipment not suitable for on-site, real-time environmental analysis. Here we demonstrate a miniaturized, autonomous bioelectronic sensing system (BESSY) suitable for deployment for instantaneous and continuous sensing applications. We developed a 2x2 cm footprint, low power, two-channel, three-electrode electrochemical potentiostat which wirelessly transmits data for on-site microbial sensing. Furthermore, we designed a new way of fabricating self-contained, submersible, miniaturized reactors (m-reactors) to encapsulate the bacteria, working, and counter electrodes. We have validated the BESSY’s ability to specifically detect a chemical amongst environmental perturbations using differential current measurements. This work paves the way for in situ microbial sensing outside of a controlled laboratory environment.
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He S, Barco RA, Emerson D, Roden EE. Comparative Genomic Analysis of Neutrophilic Iron(II) Oxidizer Genomes for Candidate Genes in Extracellular Electron Transfer. Front Microbiol 2017; 8:1584. [PMID: 28871245 PMCID: PMC5566968 DOI: 10.3389/fmicb.2017.01584] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/04/2017] [Indexed: 11/13/2022] Open
Abstract
Extracellular electron transfer (EET) is recognized as a key biochemical process in circumneutral pH Fe(II)-oxidizing bacteria (FeOB). In this study, we searched for candidate EET genes in 73 neutrophilic FeOB genomes, among which 43 genomes are complete or close-to-complete and the rest have estimated genome completeness ranging from 5 to 91%. These neutrophilic FeOB span members of the microaerophilic, anaerobic phototrophic, and anaerobic nitrate-reducing FeOB groups. We found that many microaerophilic and several anaerobic FeOB possess homologs of Cyc2, an outer membrane cytochrome c originally identified in Acidithiobacillus ferrooxidans. The "porin-cytochrome c complex" (PCC) gene clusters homologous to MtoAB/PioAB are present in eight FeOB, accounting for 19% of complete and close-to-complete genomes examined, whereas PCC genes homologous to OmbB-OmaB-OmcB in Geobacter sulfurreducens are absent. Further, we discovered gene clusters that may potentially encode two novel PCC types. First, a cluster (tentatively named "PCC3") encodes a porin, an extracellular and a periplasmic cytochrome c with remarkably large numbers of heme-binding motifs. Second, a cluster (tentatively named "PCC4") encodes a porin and three periplasmic multiheme cytochromes c. A conserved inner membrane protein (IMP) encoded in PCC3 and PCC4 gene clusters might be responsible for translocating electrons across the inner membrane. Other bacteria possessing PCC3 and PCC4 are mostly Proteobacteria isolated from environments with a potential niche for Fe(II) oxidation. In addition to cytochrome c, multicopper oxidase (MCO) genes potentially involved in Fe(II) oxidation were also identified. Notably, candidate EET genes were not found in some FeOB, especially the anaerobic ones, probably suggesting EET genes or Fe(II) oxidation mechanisms are different from the searched models. Overall, based on current EET models, the search extends our understanding of bacterial EET and provides candidate genes for future research.
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Affiliation(s)
- Shaomei He
- Department of Geoscience, University of Wisconsin-MadisonMadison, WI, United States.,NASA Astrobiology Institute, University of WisconsinMadison, WI, United States.,Department of Bacteriology, University of Wisconsin-MadisonMadison, WI, United States
| | - Roman A Barco
- Bigelow Laboratory for Ocean SciencesEast Boothbay Harbor, ME, United States.,Department of Earth Sciences, University of Southern CaliforniaLos Angeles, CA, United States
| | - David Emerson
- Bigelow Laboratory for Ocean SciencesEast Boothbay Harbor, ME, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-MadisonMadison, WI, United States.,NASA Astrobiology Institute, University of WisconsinMadison, WI, United States
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Abstract
Bacteria require iron for growth, with only a few reported exceptions. In many environments, iron is a limiting nutrient for growth and high affinity uptake systems play a central role in iron homeostasis. However, iron can also be detrimental to cells when it is present in excess, particularly under aerobic conditions where its participation in Fenton chemistry generates highly reactive hydroxyl radicals. Recent results have revealed a critical role for iron efflux transporters in protecting bacteria from iron intoxication. Systems that efflux iron are widely distributed amongst bacteria and fall into several categories: P1B-type ATPases, cation diffusion facilitator (CDF) proteins, major facilitator superfamily (MFS) proteins, and membrane bound ferritin-like proteins. Here, we review the emerging role of iron export in both iron homeostasis and as part of the adaptive response to oxidative stress.
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Affiliation(s)
- Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.
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