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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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Ding Q, Liu Q, Zhang Y, Li F, Song H. Modular Engineering Strategy to Redirect Electron Flux into the Electron-Transfer Chain for Enhancing Extracellular Electron Transfer in Shewanella oneidensis. ACS Synth Biol 2023; 12:471-481. [PMID: 36457250 DOI: 10.1021/acssynbio.2c00408] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Efficient extracellular electron transfer (EET) of exoelectrogens is critical for practical applications of various bioelectrochemical systems. However, the low efficiency of electron transfer remains a major bottleneck. In this study, a modular engineering strategy, including broadening the sources of the intracellular electron pool, enhancing intracellular nicotinamide adenine dinucleotide (NADH) regeneration, and promoting electron release from electron pools, was developed to redirect electron flux into the electron transfer chain in Shewanella oneidensis MR-1. Among them, four genes include gene SO1522 encoding a lactate transporter for broadening the sources of the intracellular electron pool, gene gapA encoding a glyceraldehyde-3-phosphate dehydrogenase and gene mdh encoding a malate dehydrogenase in the central carbon metabolism for enhancing intracellular NADH regeneration, and gene ndh encoding NADH dehydrogenase on the inner membrane for releasing electrons from intracellular electron pools into the electron-transport chain. Upon assembly of the four genes, electron flux was directly redirected from the electron donor to the electron-transfer chain, achieving 62% increase in intracellular NADH levels, which resulted in a 3.5-fold enhancement in the power density from 59.5 ± 3.2 mW/m2 (wild type) to 270.0 ± 12.7 mW/m2 (recombinant strain). This study confirmed that redirecting electron flux from the electron donor to the electron-transfer chain is a viable approach to enhance the EET rate of S. oneidensis.
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Affiliation(s)
- Qinran Ding
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Qijing Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Yan Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
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Yang J, Zhao D, Liu T, Zhang S, Wang W, Yan L, Gu JD. Growth and genome-based insights of Fe(III) reduction of the high-temperature and NaCl-tolerant Shewanella xiamenensis from Changqing oilfield of China. Front Microbiol 2022; 13:1028030. [PMID: 36545192 PMCID: PMC9760863 DOI: 10.3389/fmicb.2022.1028030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/17/2022] [Indexed: 12/09/2022] Open
Abstract
Introduction A facultative anaerobe bacterium Shewanella xiamenensis CQ-Y1 was isolated from the wastewater of Changqing oilfield in Shaanxi Province of China. Shewanella is the important dissimilatory metal-reducing bacteria. It exhibited a well potential application in biodegradation and bioremediation. Methods Genome sequencing, assembling and functional annotation were conducted to explore the genome information of CQ-Y1. The effect of temperatures and NaCl concentrations on the CQ-Y1 growth and Fe(III) reduction were investigated by UV visible spectrophotometry, SEM and XRD. Results Genomic analysis revealed its complete genome was a circular chromosome of 4,710,887 bp with a GC content of 46.50% and 4,110 CDSs genes, 86 tRNAs and 26 rRNAs. It contains genes encoding for Na+/H+ antiporter, K+/Cl- transporter, heat shock protein associated with NaCl and high-temperature resistance. The presence of genes related to flavin, Cytochrome c, siderophore, and other related proteins supported Fe(III) reduction. In addition, CQ-Y1 could survive at 10% NaCl (w/v) and 45°C, and temperature showed more pronounced effects than NaCl concentration on the bacterial growth. The maximum Fe(III) reduction ratio of CQ-Y1 reached 70.1% at 30°C without NaCl, and the reduction reaction remained active at 40°C with 3% NaCl (w/v). NaCl concentration was more effective than temperature on microbial Fe(III) reduction. And the reduction products under high temperature and high NaCl conditions were characterized as Fe3(PO4)2, FeCl2 and Fe(OH)2. Discussion Accordingly, a Fe(III) reduction mechanism of CQ-Y1 mediated by Cytochrome c and flavin was hypothesised. These findings could provide information for a better understanding of the origin and evolution of genomic and metabolic diversity of S. xiamenensis.
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Affiliation(s)
- Jiani Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Tao Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China,Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China,Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China,*Correspondence: Lei Yan,
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion – Israel Institute of Technology, Shantou, Guangdong, China,Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion – Israel Institute of Technology, Shantou, Guangdong, China
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Domínguez-Maqueda M, Pérez-Gómez O, Grande-Pérez A, Esteve C, Seoane P, Tapia-Paniagua ST, Balebona MC, Moriñigo MA. Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11. PeerJ 2022; 10:e14248. [PMID: 36312754 PMCID: PMC9610664 DOI: 10.7717/peerj.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Shewanella putrefaciens Pdp11 is a strain described as a probiotic for use in aquaculture. However, S. putrefaciens includes strains reported to be pathogenic or saprophytic to fish. Although the probiotic trait has been related to the presence of a group of genes in its genome, the existence of plasmids that could determine the probiotic or pathogenic character of this bacterium is unknown. In the present work, we searched for plasmids in several strains of S. putrefaciens that differ in their pathogenic and probiotic character. Under the different conditions tested, plasmids were only found in two of the five pathogenic strains, but not in the probiotic strain nor in the two saprophytic strains tested. Using a workflow integrating Sanger and Illumina reads, the complete consensus sequences of the plasmids were obtained. Plasmids differed in one ORF and encoded a putative replication initiator protein of the repB family, as well as proteins related to plasmid stability and a toxin-antitoxin system. Phylogenetic analysis showed some similarity to functional repB proteins of other Shewanella species. The implication of these plasmids in the probiotic or pathogenic nature of S. putrefaciens is discussed.
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Affiliation(s)
| | | | - Ana Grande-Pérez
- Área de Genética, Universidad de Málaga, Málaga, Spain,Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Consuelo Esteve
- Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - Pedro Seoane
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, Madrid, Spain,Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
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Fan Y, Tang Q, Sun H, Yu H. A designed plasmid‐transition strategy enables rapid construction of robust and versatile synthetic exoelectrogens for environmental applications. Environ Microbiol 2022; 24:5292-5305. [DOI: 10.1111/1462-2920.16181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Yang‐Yang Fan
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences University of Science and Technology of China Hefei China
- Department of Environmental Science and Engineering University of Science & Technology of China Hefei China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology Anhui University Hefei China
| | - Qiang Tang
- Department of Environmental Science and Engineering University of Science & Technology of China Hefei China
| | - Hong Sun
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences University of Science and Technology of China Hefei China
- Department of Environmental Science and Engineering University of Science & Technology of China Hefei China
| | - Han‐Qing Yu
- Department of Environmental Science and Engineering University of Science & Technology of China Hefei China
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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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Engineering S. oneidensis for Performance Improvement of Microbial Fuel Cell-a Mini Review. Appl Biochem Biotechnol 2020; 193:1170-1186. [PMID: 33200267 DOI: 10.1007/s12010-020-03469-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/09/2020] [Indexed: 02/02/2023]
Abstract
Microbial fuel cell (MFC) is a promising technology that utilizes exoelectrogens cultivated in the form of biofilm to generate power from various types of sources supplied. A metal-reducing pathway is utilized by these organisms to transfer electrons obtained from the metabolism of substrate from anaerobic respiration extracellularly. A widely established model organism that is capable of extracellular electron transfer (EET) is Shewanella oneidensis. This review highlights the strategies used in the transformation of S. oneidensis and the recent development of MFC in terms of intervention through genetic modifications. S. oneidensis was genetically engineered for several aims including the study on the underlying mechanisms of EET, and the enhancement of power generation and wastewater treating potential when used in an MFC. Through engineering S. oneidensis, genes responsible for EET are identified and strategies on enhancing the EET efficiency are studied. Overexpressing genes related to EET to enhance biofilm formation, mediator biosynthesis, and respiration appears as one of the common approaches.
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Yi YC, Ng IS. Establishment of toolkit and T7RNA polymerase/promoter system in Shewanella oneidensis MR-1. J Taiwan Inst Chem Eng 2020. [DOI: 10.1016/j.jtice.2020.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Suo D, Fang Z, Yu Y, Yong Y. Synthetic curli enables efficient microbial electrocatalysis with stainless‐steel electrode. AIChE J 2019. [DOI: 10.1002/aic.16897] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Di Suo
- Biofuels Institute, School of Environment and Safety EngineeringJiangsu University Zhenjiang China
| | - Zhen Fang
- Biofuels Institute, School of Environment and Safety EngineeringJiangsu University Zhenjiang China
| | - Yang‐Yang Yu
- Biofuels Institute, School of Environment and Safety EngineeringJiangsu University Zhenjiang China
| | - Yang‐Chun Yong
- Biofuels Institute, School of Environment and Safety EngineeringJiangsu University Zhenjiang China
- Zhenjiang Key Laboratory of Advanced Sensing Materials and Devices, School of Mechanical Engineering, Jiangsu University Zhenjiang China
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Huang BC, Yi YC, Chang JS, Ng IS. Mechanism study of photo-induced gold nanoparticles formation by Shewanella oneidensis MR-1. Sci Rep 2019; 9:7589. [PMID: 31110216 PMCID: PMC6527576 DOI: 10.1038/s41598-019-44088-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/09/2019] [Indexed: 11/09/2022] Open
Abstract
Shewanella oneidensis MR-1, a bioelectricity generating bacterium, is broadly used in bioremediation, microbial fuel cell and dissimilatory reduction and recovery of precious metals. Herein, we report for the first time that photo induction as a trigger to stimulate gold nanoparticles (Au@NPs) formation by MR-1, with wavelength and light intensity as two key variables. Results indicated that sigmoidal model is the best fit for Au@NPs formation at various wavelengths (with R2 > 0.97). Light intensity in terms of photosynthetic photon flux density (PPFD) critically influences the rate constant in the low-light intensity region (PPFD < 20), while wavelength controls the maximum rate constant in the high-light region (PPFD > 20). By deletion of Mtr pathway genes in MR-1, we proposed the mechanism for light induced Au@NP formation is the excitation effect of light on certain active groups and extracellular polymeric substances (EPS) on the cell surface. Also, the release of electrons from proteins and co-enzyme complexes enhance electron generation. To the best of our knowledge, this is the first-attempt to explore the effect of photo-induction on Au@NPs production by MR-1, which provides an alternative cost-effective and eco-friendly process in green chemical industry.
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Affiliation(s)
- Bo Chuan Huang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, ROC, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, ROC, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, ROC, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, ROC, Taiwan.
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