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Liu T, Zheng X, Guo M, Bao D, Yang H. The genotoxicity impact of heavy metals on the Escherichia coli. ENVIRONMENTAL TECHNOLOGY 2024; 45:4585-4597. [PMID: 37727136 DOI: 10.1080/09593330.2023.2260120] [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: 03/31/2023] [Accepted: 08/11/2023] [Indexed: 09/21/2023]
Abstract
In present work, the genotoxicity of Hg2+, Ag+, Cr6+, Ni2+, Pb2+, Co2+, Mn2+, Zn2+, and Cr3+ was investigated via a quantitative toxicogenomics assay, to understand the toxic mechanism of heavy metals with greater depth. Under the experimental conditions, Hg2+, Ag+, and Cr6+ showed a more serious toxic impact on the expression of functional genes (eg., oxyR, katG, grxA, osmE, emrE, dinG) than Ni2+, Pb2+, Co2+, Mn2+, Zn2+, and Cr3+, while the protein, oxidative, and membrane stress response pathways were more sensitive to the toxicity of Hg2+, Ag+, and Cr6+ than the DNA and general stress response pathways. Compared with the other kinds of heavy metals, Ni2+, Pb2+, Co2+, and Mn2+ altered the expression of functional genes (uvrY, recX, mutY, and sbmC) related to the DNA stress response pathways more seriously, while Zn2+ and Cr3+ changed the expression of the functional genes (yfjG, ydgL, ssrA, and osmC) associated with the general stress response pathway more significantly. Meanwhile, the toxicity of Ni2+, Pb2+, Co2+, and Mn2+ was slightly higher than that of Zn2+ and Cr3+ in terms of the total value of transcriptional effect level Index (TELI) by detecting the promoter activities of different functional genes. In addition, to survive the toxicity of heavy metals, the expression of multidrug efflux genes (ydgL, cyoA, emrA, and emrE) and toxicity-resistant genes (Ion, dnaJ, clpB, mutY, dnaK, rpoD, sbmC) mainly functioned.
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Affiliation(s)
- Tong Liu
- School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, People's Republic of China
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Xing Zheng
- School of Environment and Natural Resources, Zhejiang University of Science & Technology, Hangzhou, People's Republic of China
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
- National Supervision & Inspection Center of Environmental Protection Equipment Quality, Jiangsu, Yixing, People's Republic of China
| | - Menghan Guo
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Dongguan Bao
- Shanghai Hanyuan Engineering & Technology Company Limited, Shanghai, People's Republic of China
| | - Heyun Yang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, People's Republic of China
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Ji L, Chang X, Wang L, Fu X, Lai W, Zheng L, Li Q, Xing Y, Yang Z, Guan Y, Yang F. Insights into the biodegradation of pentachlorobiphenyl by Microbacterium paraoxydans: proteomic and metabolomic studies. Front Microbiol 2024; 15:1389805. [PMID: 38933025 PMCID: PMC11203399 DOI: 10.3389/fmicb.2024.1389805] [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: 02/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full remediation of environments afflicted by the complex pollution of polychlorinated biphenyls (PCBs). In this research, a new PentaCB-degrading bacterium Microbacterium paraoxydans that has not been reported was obtained using enzymatic screening method. The characteristics of its intracellular enzymes, proteome and metabolome variation during PentaCB degradation were investigated systematically compared to non-PentaCB conditions. The findings indicate that the degradation rate of PentaCB (1 mg/L) could reach 23.9% within 4 hours and achieve complete degradation within 12 hours, with the mixture of intracellular enzymes being most effective at a pH of 6.0. During the biodegradation of PentaCB, the 12 up-regulated proteins characterized included ABC transporter PentaCB-binding protein, translocase protein TatA, and signal peptidase I (SPase I), indicating the presence of functional proteins for PentaCB degradation in both the cytoplasm and the outer surface of the cytoplasmic membrane. Furthermore, five differentially enriched metabolites were strongly associated with the aforementioned proteins, especially the up-regulated 1, 2, 4-benzenetriol which feeds into multiple degradation pathways of benzoate, chlorocyclohexane, chlorobenzene and aminobenzoate. These relevant results help to understand and speculate the complex mechanisms regarding PentaCB degradation by M. paraoxydans, which have both theoretical and practical implications for PCB bioremediation.
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Affiliation(s)
- Lei Ji
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xiaoyu Chang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Leilei Wang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xiaowen Fu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Wenkai Lai
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Liwen Zheng
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Qi Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yingna Xing
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Zhongfeng Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yuyao Guan
- Department of Pharmacy, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fenglong Yang
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
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Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [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: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
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Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Dey P, Malik A, Singh DK, Haange SB, von Bergen M, Jehmlich N. Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique. Front Microbiol 2022; 13:872576. [PMID: 35756008 PMCID: PMC9221998 DOI: 10.3389/fmicb.2022.872576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.
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Affiliation(s)
- Priyadarshini Dey
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Department of Biotechnology, MS Ramaiah Institute of Technology, Bengaluru, India
| | - Anushree Malik
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Dileep Kumar Singh
- Department of Zoology, Faculty of Science, University of Delhi, New Delhi, India
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity, Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- *Correspondence: Nico Jehmlich,
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Tabassum N, Islam N, Ahmed S. Progress in microbial fuel cells for sustainable management of industrial effluents. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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赵 宇. Applications of Systems Biology in Bioremediation. INTERNATIONAL JOURNAL OF ECOLOGY 2021. [DOI: 10.12677/ije.2021.104062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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de Souza NA, Ramaiah N, Damare S, Furtado B, Mohandass C, Patil A, De Lima M. Differential Protein Expression in Shewanella seohaensis Decolorizing Azo Dyes. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164615666180731110845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Microbial remediation is an ecologically safe alternative to controlling environmental pollution caused by toxic aromatic compounds including azo dyes. Marine bacteria show excellent potential as agents of bioremediation. However, a lack of understanding of the entailing mechanisms of microbial degradation often restricts its wide-scale and effective application.Objective:To understand the changes in a bacterial proteome profile during azo dye decolorization.Methods:In this study, we tested a Gram-negative bacterium, Shewanella seohaensis NIODMS14 isolated from an estuarine environment and grown in three different azo dyes (Reactive Black 5 (RB5), Reactive Green 19 (RG19) and Reactive Red 120 (RR120)). The unlabeled bacterial protein samples extracted during the process of dye decolorization were subject to mass spectrometry. Relative protein quantification was determined by comparing the resultant MS/MS spectra for each protein.Results:Maximum dye decolorization of 98.31% for RB5, 91.49% for RG19 and 97.07% for RR120 at a concentration of 100 mg L-1 was observed. The liquid chromatography-mass spectrometry - Quadrupole Time of Flight (LCMS-QToF) analysis revealed that as many as 29 proteins were up-regulated by 7 hours of growth and 17 by 24 hours of growth. Notably, these were common across the decolorized solutions of all three azo dyes. In cultures challenged with the azo dyes, the major class of upregulated proteins was cellular oxidoreductases and an alkyl hydroperoxide reductase (SwissProt ID: A9KY42).Conclusion:The findings of this study on the bacterial proteome profiling during the azo dye decolorization process are used to highlight the up-regulation of important proteins that are involved in energy metabolism and oxido-reduction pathways. This has important implications in understanding the mechanism of azo dye decolorization by Shewanella seohaensis.
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Affiliation(s)
- Nadine Ana de Souza
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Nagappa Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Samir Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Bliss Furtado
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Chellandi Mohandass
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Anushka Patil
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Marsha De Lima
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Annamalai S, Santhanam M, Selvaraj S, Sundaram M, Pandian K, Pazos M. "Green technology": Bio-stimulation by an electric field for textile reactive dye contaminated agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:1649-1657. [PMID: 29054631 DOI: 10.1016/j.scitotenv.2017.10.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
The aim of the study is to degrade pollutants as well as to increase the fertility of agricultural soil by starch enhancing electrokinetic (EKA) and electro-bio-stimulation (EBS) processes. Starch solution was used as an anolyte and voltage gradient was about 0.5V/cm. The influence of bacterial mediated process was evaluated in real contaminated farming soil followed by pilot scale experiment. The in-situ formation of β-cyclodextrin from starch in the treatments had also influence on the significant removal of the pollutants from the farming soil. The conductivity of the soil was effectively reduced from 15.5dS/m to 1.5dS/m which corroborates well with the agricultural norms. The bio-stimulation was confirmed by the increase of the phosphorus content in the treated soil. Finally, phytotoxicity assays demonstrated the viability of the developed technique for soil remediation because plant germination percentage was higher in the treated soil in comparison to untreated soil.
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Affiliation(s)
- Sivasankar Annamalai
- CSIR-Central Electrochemical Research Institute, Karaikudi 630 003, India; Academy of Scientific and Innovative Research, Karaikudi, Tamil Nadu 630 003, India.
| | - Manikandan Santhanam
- CSIR-Central Electrochemical Research Institute, Karaikudi 630 003, India; Academy of Scientific and Innovative Research, Karaikudi, Tamil Nadu 630 003, India
| | - Subbulakshmi Selvaraj
- CSIR-Central Electrochemical Research Institute, Karaikudi 630 003, India; Academy of Scientific and Innovative Research, Karaikudi, Tamil Nadu 630 003, India
| | | | - Kannan Pandian
- Dryland Agricultural Research Station, Tamilnadu Agricultural University, Chettinad 630 102, India
| | - Marta Pazos
- Department of Chemical Engineering, University of Vigo, Lagoas-Marcosende 36310, Spain
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Liao HY, Chien CC, Tang P, Chen CC, Chen CY, Chen SC. The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp. JOURNAL OF HAZARDOUS MATERIALS 2018; 349:79-90. [PMID: 29414755 DOI: 10.1016/j.jhazmat.2018.01.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 06/08/2023]
Abstract
Citrobacter sp. has been shown to degrade 2,4,6-trinitrotoluene (TNT). However, the mechanism of its TNT biodegradation is poorly understood. An integrated proteome and transcriptome analysis was performed for investigating the differential genes and differential proteins in bacterial growth at the onset of experiments and after 12 h treatment with TNT. With the RNA sequencing, we found a total of 3792 transcripts and 569 differentially expressed genes (≥2 fold, P < 0.05) by. Genes for amino acid transport, cellular metabolism and stress-shock proteins were up-regulated, while carbohydrate transport and metabolism were down-regulated. A total of 42 protein spots (≥1.5 fold, P < 0.05) showed differential expression on two-dimensional gel electrophoresis and these proteins were identified by mass spectrometry. The most prominent proteins up-regulated were involved in energy production and conversion, amino acid transport and metabolism, posttranslational modification, protein turnover and chaperones. Proteins involved in carbohydrate transport and metabolism were down-regulated. Most notably, we observed that nemA encoding N-ethylmaleimide reductase was the most up-regulated gene involved in TNT degradation, and further proved that it can transform TNT to 4-amino-2,6-dinitrotoluene (4-ADNT) and 2-amino-4,6-dinitrotoluene (2-ADNT). This study highlights the molecular mechanisms of Citrobacter sp. for TNT removal.
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Affiliation(s)
- Hung-Yu Liao
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135, Yuantung Rd., Jhongli City, Taoyuan, 32003, Taiwan
| | - Petrus Tang
- Department of Parasitology, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dis., Taoyuan City, 33302, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, No.116, Heping 1st Rd., Lingya District, Kaohsiung City, 80201, Taiwan
| | - Chin-Yu Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan.
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Shuona C, Hua Y, Jingjing C, Hui P, Zhi D. Physiology and bioprocess of single cell of Stenotrophomonas maltophilia in bioremediation of co-existed benzo[a]pyrene and copper. JOURNAL OF HAZARDOUS MATERIALS 2017; 321:9-17. [PMID: 27607928 DOI: 10.1016/j.jhazmat.2016.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/19/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and heavy metals are generally present in mixtures in the e-waste dismantling areas, posing serious health risk to the local people. Bioremediation has been considered as a promising approach for PAHs and heavy metals removal. In this study, we applied flow cytometry to obtain a better understanding of membrane potential (MP), apoptosis and cell cycle of Stenotrophomonas maltophilia affected by combined pollutants of benzo[a]pyrene(BaP) and Cu(II). The results showed that BaP was the main factor damaging the cell membrane and influencing the MP. S. maltophilia could even protect against upsetting situation by encouraging early apoptosis, whereby compromised cells committed suicide, as a result, which, in turn, facilitated the metabolism of the bacteria with high-vitality. Furthermore, even if the bacterial cell division was blocked and stopped reproduction, a large number of key enzymes inside cells could still be used for degradation of BaP. The expression of protein related to the transport and metabolism of BaP, regulation of redox reactions and phosphorylation in bacterial cell during bioprocess were evident different.
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Affiliation(s)
- Chen Shuona
- College of Natural Resources and Environment of South China Agricultural University, Guangzhou 510642, China
| | - Yin Hua
- Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education; School of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
| | - Chang Jingjing
- College of Natural Resources and Environment of South China Agricultural University, Guangzhou 510642, China
| | - Peng Hui
- Department of Chemistry, School of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Dang Zhi
- Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education; School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
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BOCIAN A, HUS K, JAROMIN M, TYRKA M, ŁYSKOWSKI A. Identification of proteins differentially accumulated in Enterococcus faecalis under acrylamide exposure. Turk J Biol 2017. [DOI: 10.3906/biy-1606-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Yang S, Wen X, Shi Y, Liebner S, Jin H, Perfumo A. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments. Sci Rep 2016; 6:37473. [PMID: 27886221 PMCID: PMC5122841 DOI: 10.1038/srep37473] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023] Open
Abstract
Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.
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Affiliation(s)
- Sizhong Yang
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, China.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Xi Wen
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.,College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Yulan Shi
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, China
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Huijun Jin
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, China
| | - Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
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Metabolic Fingerprinting of Pseudomonas putida DOT-T1E Strains: Understanding the Influence of Divalent Cations in Adaptation Mechanisms Following Exposure to Toluene. Metabolites 2016; 6:metabo6020014. [PMID: 27128955 PMCID: PMC4931545 DOI: 10.3390/metabo6020014] [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: 02/16/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas putida strains can adapt and overcome the activity of toxic organic solvents by the employment of several resistant mechanisms including efflux pumps and modification to lipopolysaccharides (LPS) in their membranes. Divalent cations such as magnesium and calcium play a crucial role in the development of solvent tolerance in bacterial cells. Here, we have used Fourier transform infrared (FT-IR) spectroscopy directly on cells (metabolic fingerprinting) to monitor bacterial response to the absence and presence of toluene, along with the influence of divalent cations present in the growth media. Multivariate analysis of the data using principal component-discriminant function analysis (PC-DFA) showed trends in scores plots, illustrating phenotypic alterations related to the effect of Mg(2+), Ca(2+) and toluene on cultures. Inspection of PC-DFA loadings plots revealed that several IR spectral regions including lipids, proteins and polysaccharides contribute to the separation in PC-DFA space, thereby indicating large phenotypic response to toluene and these cations. Finally, the saturated fatty acid ratio from the FT-IR spectra showed that upon toluene exposure, the saturated fatty acid ratio was reduced, while it increased in the presence of divalent cations. This study clearly demonstrates that the combination of metabolic fingerprinting with appropriate chemometric analysis can result in practicable knowledge on the responses of important environmental bacteria to external stress from pollutants such as highly toxic organic solvents, and indicates that these changes are manifest in the bacterial cell membrane. Finally, we demonstrate that divalent cations improve solvent tolerance in P. putida DOT‑T1E strains.
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Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Muhamadali H, Rattray NJW, Webb C, Goodacre R. Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry. Metabolomics 2016; 12:112. [PMID: 27398079 PMCID: PMC4916193 DOI: 10.1007/s11306-016-1054-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/04/2016] [Indexed: 01/09/2023]
Abstract
INTRODUCTION An exceptionally interesting stress response of Pseudomonas putida strains to toxic substances is the induction of efflux pumps that remove toxic chemical substances from the bacterial cell out to the external environment. To exploit these microorganisms to their full potential a deeper understanding of the interactions between the bacteria and organic solvents is required. Thus, this study focuses on investigation of metabolic changes in P. putida upon exposure to toluene. OBJECTIVE Investigate observable metabolic alterations during interactions of three strains of P. putida (DOT-T1E, and its mutants DOT-T1E-PS28 and DOT-T1E-18) with the aromatic hydrocarbon toluene. METHODS The growth profiles were measured by taking optical density (OD) measurement at 660 nm (OD660) at various time points during incubation. For fingerprinting analysis, Fourier-transform infrared (FT-IR) spectroscopy was used to investigate any phenotypic changes resulting from exposure to toluene. Metabolic profiling analysis was performed using gas chromatography-mass spectrometry (GC-MS). Principal component-discriminant function analysis (PC-DFA) was applied to the FT-IR data while multiblock principal component analysis (MB-PCA) and N-way analysis of variance (N-way ANOVA) were applied to the GC-MS data. RESULTS The growth profiles demonstrated the effect of toluene on bacterial cultures and the results suggest that the mutant P. putida DOT-T1E-18 was more sensitive (significantly affected) to toluene compared to the other two strains. PC-DFA on FT-IR data demonstrated the differentiation between different conditions of toluene on bacterial cells, which indicated phenotypic changes associated with the presence of the solvent within the cell. Fifteen metabolites associated with this phenotypic change, in P. putida due to exposure to solvent, were from central metabolic pathways. Investigation of MB-PCA loading plots and N-way ANOVA for condition | strain × time blocking (dosage of toluene) suggested ornithine as the most significant compound that increased upon solvent exposure. CONCLUSION The combination of metabolic fingerprinting and profiling with suitable multivariate analysis revealed some interesting leads for understanding the mechanism of Pseudomonas strains response to organic solvent exposure.
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Affiliation(s)
- Ali Sayqal
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Drupad K. Trivedi
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Najla AlMasoud
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - David I. Ellis
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Nicholas J. W. Rattray
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Carole Webb
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
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Bastida F, Jehmlich N, Lima K, Morris BEL, Richnow HH, Hernández T, von Bergen M, García C. The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment. J Proteomics 2015. [PMID: 26225916 DOI: 10.1016/j.jprot.2015.07.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in semiarid soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted semiarid soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.
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Affiliation(s)
- F Bastida
- Department of Soil and Water Conservation, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus Universitario de Espinardo, Aptdo. de Correos 164, Espinardo, 30100 Murcia, Spain; Department of Agroforestry Technology and Science and Genetics, School of Advanced Agricultural Engineering, Castilla La Mancha University, Campus Universitario s/n, Albacete, Spain.
| | - N Jehmlich
- Department of Proteomics, Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - K Lima
- Department of Soil and Water Conservation, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus Universitario de Espinardo, Aptdo. de Correos 164, Espinardo, 30100 Murcia, Spain
| | - B E L Morris
- Dow Microbial Control, Dow Europe GmbH, Bachtobelstrasse 3, 8810 Horgen, Switzerland
| | - H H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - T Hernández
- Department of Soil and Water Conservation, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus Universitario de Espinardo, Aptdo. de Correos 164, Espinardo, 30100 Murcia, Spain
| | - M von Bergen
- Department of Proteomics, Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany; Department of Metabolomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - C García
- Department of Soil and Water Conservation, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus Universitario de Espinardo, Aptdo. de Correos 164, Espinardo, 30100 Murcia, Spain
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Vandera E, Samiotaki M, Parapouli M, Panayotou G, Koukkou AI. Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose. J Proteomics 2014; 113:73-89. [PMID: 25257624 DOI: 10.1016/j.jprot.2014.08.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/18/2014] [Accepted: 08/22/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED In the present study, by applying comparative quantitative proteomics, we investigated the metabolic adaptation of Arthrobacter phenanthrenivorans Sphe3 when using phenanthrene, phthalate, glucose or glucose plus phenanthrene as sole carbon and energy sources. More than a third of the total Sphe3 proteins, with function prediction within the genome, were identified with confidence. Proteomic analysis data and annotated genomic information coincide, allowing us to clarify the phenanthrene catabolic pathway. We confirmed the implication of several proteins in aromatic substrate degradation by identifying those mediating the initial ring-hydroxylation and ring cleavage of phenanthrene to phthalate, phthalate degradation, as well as ortho- and meta-protocatechuate catabolism. Repression of catabolic genes by glucose was observed by both proteomic and transcriptional analyses. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in substrate and amino acid metabolism, stress response, detoxification and membrane and cell wall metabolism. Uptake and transport associated proteins differ in the substrates used, indicating the use of different uptake mechanisms for transport of each compound in the Sphe3 cells. Our results also suggest the activation of a glyoxylate shunt in the presence of aromatic compounds, based on the up-regulation of the key enzymes of this pathway. BIOLOGICAL SIGNIFICANCE A. phenanthrenivorans Sphe3, isolated from a creosote contaminated soil in Greece, can grow on phenanthrene as the sole source of carbon and energy. To explore the phenanthrene catabolic pathway by determining the key proteins involved in this pathway, as well as the global changes in proteins due to the adaptive response of Sphe3 cells grown on different substrates, we applied a gel-free quantitative proteomic analysis using nanoLC-MS/MS. To our knowledge this is the first study of comparative global proteomic changes occurring in the Sphe3 cells under exposure in different nutritional environments. The extended proteomic changes observed in Sphe3 grown on different substrates provide an insight in the complex interactions occurring in the presence of aromatic compounds and could serve as a basis for further investigations intended to elucidate the general regulatory mechanism by which Sphe3 adapts to such xenobiotic environments. This may light the way for more efficient engineering of bacteria towards more effective bioremediation applications.
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Affiliation(s)
- Elpiniki Vandera
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Athens, Greece.
| | - Maria Parapouli
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Athens, Greece
| | - Anna Irini Koukkou
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece.
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Bioresources for control of environmental pollution. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 147:137-83. [PMID: 25312333 DOI: 10.1007/10_2014_276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Environmental pollution is one of the biggest threats to human beings. For practical reasons it is not possible to stop most of the activities responsible for environmental pollution; rather we need to eliminate the pollutants. In addition to other existing means, biological processes can be utilized to get rid of toxic pollutants. Degradation, removal, or deactivation of pollutants by biological means is known as bioremediation. Nature itself has several weapons to deal with natural wastage and some of them are equally active for eliminating nonnatural pollutants. Several plants, microorganisms, and some lower eukaryotes utilize environmental pollutants as nutrients and some of them are very efficient for decontaminating specific types of pollutants. If exploited properly, these natural resources have enough potential to deal with most elements of environmental pollution. In addition, several artificial microbial consortia and genetically modified organisms with high bioremediation potential were developed by application of advanced scientific tools. On the other hand, natural equilibria of ecosystems are being affected by human intervention. Rapid population growth, urbanization, and industrialization are destroying ecological balances and the natural remediation ability of the Earth is being compromised. Several potential bioremediation tools are also being destroyed by biodiversity destruction of unexplored ecosystems. Pollution management by bioremediation is highly dependent on abundance, exploration, and exploitation of bioresources, and biodiversity is the key to success. Better pollution management needs the combined actions of biodiversity conservation, systematic exploration of natural resources, and their exploitation with sophisticated modern technologies.
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Akondi K, Lakshmi V. Emerging Trends in Genomic Approaches for Microbial Bioprospecting. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:61-70. [DOI: 10.1089/omi.2012.0082] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- K.B. Akondi
- Department of Applied Microbiology, Sri Padmavati Women's University, Tirupati, India
| | - V.V. Lakshmi
- Department of Applied Microbiology, Sri Padmavati Women's University, Tirupati, India
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The Biotechnological Potential of Corynebacterium glutamicum, from Umami to Chemurgy. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Megharaj M, Ramakrishnan B, Venkateswarlu K, Sethunathan N, Naidu R. Bioremediation approaches for organic pollutants: a critical perspective. ENVIRONMENT INTERNATIONAL 2011; 37:1362-75. [PMID: 21722961 DOI: 10.1016/j.envint.2011.06.003] [Citation(s) in RCA: 366] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 05/30/2011] [Accepted: 06/07/2011] [Indexed: 05/22/2023]
Abstract
Due to human activities to a greater extent and natural processes to some extent, a large number of organic chemical substances such as petroleum hydrocarbons, halogenated and nitroaromatic compounds, phthalate esters, solvents and pesticides pollute the soil and aquatic environments. Remediation of these polluted sites following the conventional engineering approaches based on physicochemical methods is both technically and economically challenging. Bioremediation that involves the capabilities of microorganisms in the removal of pollutants is the most promising, relatively efficient and cost-effective technology. However, the current bioremediation approaches suffer from a number of limitations which include the poor capabilities of microbial communities in the field, lesser bioavailability of contaminants on spatial and temporal scales, and absence of bench-mark values for efficacy testing of bioremediation for their widespread application in the field. The restoration of all natural functions of some polluted soils remains impractical and, hence, the application of the principle of function-directed remediation may be sufficient to minimize the risks of persistence and spreading of pollutants. This review selectively examines and provides a critical view on the knowledge gaps and limitations in field application strategies, approaches such as composting, electrobioremediation and microbe-assisted phytoremediation, and the use of probes and assays for monitoring and testing the efficacy of bioremediation of polluted sites.
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Affiliation(s)
- Mallavarapu Megharaj
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, SA 5095, Australia
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K SK, R A, Arumugam P, Berchmans S. Synthesis of gold nanoparticles: an ecofriendly approach using Hansenula anomala. ACS APPLIED MATERIALS & INTERFACES 2011; 3:1418-1425. [PMID: 21517037 DOI: 10.1021/am200443j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This work describes a bioassisted approach for the preparation of metal nanoparticles using yeast species Hansenula anomala. Gold nanoparticles were prepared using gold salt as the precursor, amine-terminated polyamidoamine dendrimer as the stabilizer, and the extracellular material from H. anomala as the bioreductant. It could also be demonstrated that, using our approach, small molecules such as cysteine can act as stabilizers as well. This synthetic approach offers a greener alternative route to the preparation of gold sols that are devoid of cellular and toxic chemical components. The ability of as-synthesized gold sol to function as biological ink for producing patterns for the analysis of fingerprints and to act as an antimicrobial reagent is evaluated. The generality of this toxin-free synthetic approach to other metals was assessed using palladium and silver.
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Affiliation(s)
- Sathish Kumar K
- Electrodics and Electrocatalysis Division, Central Electro-Chemical Research Institute, Council of Scientific and Industrial Research, Karaikudi 630006, India
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Yıldırım V, Ozcan S, Becher D, Büttner K, Hecker M, Ozcengiz G. Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure. Proteome Sci 2011; 9:12. [PMID: 21388532 PMCID: PMC3063812 DOI: 10.1186/1477-5956-9-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 03/09/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Total soluble proteome alterations of white rot fungus Phanerochaete chrysosporium in response to different doses (25, 50 and 100 μM) of Pb (II) were characterized by 2DE in combination with MALDI-TOF-MS. RESULTS Dose-dependent molecular response to Pb (II) involved a total of 14 up-regulated and 21 down-regulated proteins. The induction of an isoform of glyceraldehyde 3-phosphate dehydrogenase, alcohol dehydrogenase class V, mRNA splicing factor, ATP-dependent RNA helicase, thioredoxin reductase and actin required a Pb (II) dose of at least 50 μM. Analysis of the proteome dynamics of mid-exponential phase cells of P. chrysosporium subjected to 50 μM lead at exposure time intervals of 1, 2, 4 and 8 h, identified a total of 23 proteins in increased and 67 proteins in decreased amount. Overall, the newly induced/strongly up-regulated proteins involved in (i) amelioration of lipid peroxidation products, (ii) defense against oxidative damage and redox metabolism, (iii) transcription, recombination and DNA repair (iv) a yet unknown function represented by a putative protein. CONCLUSION The present study implicated the particular role of the elements of DNA repair, post-tanscriptional regulation and heterotrimeric G protein signaling in response to Pb (II) stress as shown for the first time for a basidiomycete.
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Affiliation(s)
- Volkan Yıldırım
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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Gou LT, Tong AP, Yan F, Yuan Z, He F, Wang W, Zhou Y, Chen LJ, Tang MH, Yang JL. Altered protein-expressing profile in hPNAS4-induced apoptosis in A549 human lung adenocarcinoma cells. J Cell Biochem 2010; 108:1211-9. [PMID: 19795389 DOI: 10.1002/jcb.22353] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human PNAS4 (hPNAS4) is a recently identified pro-apoptosis gene, which is able to induce apoptosis in A549 human lung adenocarcinoma cells following its overexpression. In this work, we investigated the changes of protein profile in hPNAS4-induced apoptosis in A549 cells through proteomic strategy consisting of two-dimensional electrophoresis (2-DE) coupled with MALDI-Q-TOF mass spectrometry. A total of 20 different proteins with more than 3.0-fold change in expression, including 5 up-regulated and 15 down-regulated proteins were successfully identified by database search. The mRNA transcription levels of the different proteins were further examined by RT-PCT. Functional analyses showed these different proteins are involved in diverse biological processes including metabolism, proteolysis, signal transduction, apoptosis, and redox regulation. Two essential apoptosis-associated protein, annexin A1 and prothymosin alpha, were confirmed by Western blot and showed consistent changes with proteomic detection. Our data provide molecular evidence and possible associated pathway in hPNAS4-induced apoptosis through proteomic strategy, which should be contributed to further investigation on biological function of hPNAS4.
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Affiliation(s)
- Lan-Tu Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan Province, China
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Biodegradation: gaining insight through proteomics. Biodegradation 2010; 21:861-79. [DOI: 10.1007/s10532-010-9361-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 04/13/2010] [Indexed: 10/19/2022]
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Singh OV, Chandel AK. Two-dimensional gel electrophoresis: discovering biomolecules for environmental bioremediation. Methods Mol Biol 2010; 599:141-156. [PMID: 19882285 DOI: 10.1007/978-1-60761-439-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Environmental contamination has been viewed as an ecological malaise for which bioremediation can be prescribed as a "perfect medicine." The solution to the problems with bioremediation lies in analyzing to what extent the microbes' physiological machinery contributes to the degradation process and which biomolecules and their mechanisms are responsible for regulatory factors within the degradation system, such as protein, metabolite, and enzymatic chemical transformation. In the post-genomic era, recent advances in proteomics have allowed us to elucidate many complex biological mechanisms. Two-dimensional gel electrophoresis (2DE) in conjunction with mass spectrometry (MS) can be utilized to identify the biomolecules and their molecular mechanisms in bioremediation. A set of highly abundant global proteins over a pI range 4-7 was separated and compared by size fractionation (25-100 kDa) on 2DE. We identified a set of catabolic proteins, enzymes, and heat shock molecular chaperones associated with the regulatory network that was found to be overexpressed under phenol-stressed conditions. This chapter also offers optimized ideal directions for 2DE, followed by easy-to-follow directions for a protein identification strategy using MALDI-TOF and targeting novel proteins/enzymes for a universal set of experiments.
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Affiliation(s)
- Om V Singh
- Division of Biological and Health Science, University of Pittsburgh-Bradford, Bradford, PA 16701, USA.
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Nicolau E, Kuhn L, Marchal R, Jouanneau Y. Proteomic investigation of enzymes involved in 2-ethylhexyl nitrate biodegradation in Mycobacterium austroafricanum IFP 2173. Res Microbiol 2009; 160:838-47. [DOI: 10.1016/j.resmic.2009.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 09/23/2009] [Accepted: 09/27/2009] [Indexed: 10/20/2022]
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Zhang W, Li F, Nie L. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. MICROBIOLOGY-SGM 2009; 156:287-301. [PMID: 19910409 DOI: 10.1099/mic.0.034793-0] [Citation(s) in RCA: 281] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in various 'omics' technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular 'omics' platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single 'omics' analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-'omics' approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous 'omics' datasets in various microbial systems and the results have demonstrated that the multi-'omics' approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental 'omics' approaches, recent application of the integrated 'omics' for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated 'omics' analyses. Online databases and bioinformatic infrastructure available for integrated 'omics' analyses are also briefly discussed.
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Affiliation(s)
- Weiwen Zhang
- Center for Ecogenomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6501, USA
| | - Feng Li
- Division of Biometrics II, Office of Biometrics/OTS/CDER/FDA, Silver Spring, MD 20993-0002, USA
| | - Lei Nie
- Division of Biometrics IV, Office of Biometrics/OTS/CDER/FDA, Silver Spring, MD 20993-0002, USA
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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A novel E. coli biosensor for detecting aromatic aldehydes based on a responsive inducible archaeal promoter fused to the green fluorescent protein. Appl Microbiol Biotechnol 2009; 82:67-77. [DOI: 10.1007/s00253-008-1771-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 10/23/2008] [Accepted: 10/25/2008] [Indexed: 10/21/2022]
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Nesatyy VJ, Suter MJF. Analysis of environmental stress response on the proteome level. MASS SPECTROMETRY REVIEWS 2008; 27:556-574. [PMID: 18553564 DOI: 10.1002/mas.20177] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers.
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Affiliation(s)
- Victor J Nesatyy
- Eawag-Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, PO Box 611, 8600 Duebendorf, Switzerland
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