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Saravanan A, Kumar PS, Ramesh B, Srinivasan S. Removal of toxic heavy metals using genetically engineered microbes: Molecular tools, risk assessment and management strategies. CHEMOSPHERE 2022; 298:134341. [PMID: 35307383 DOI: 10.1016/j.chemosphere.2022.134341] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The direct release of industrial effluent into the water and other anthropogenic activities causes water pollution. Heavy metal ions are the primary contaminant in the industrial effluents which are exceptionally toxic at low concentrations, terribly disturb the endurance equilibrium of activities in the eco-system and be remarkably hazardous to human health. Different conventional treatment methodologies were utilized for the removal of toxic pollutants from the contaminated water which has several drawbacks such as cost-ineffective and lower efficiency. Recently, genetically modified micro-organisms (GMMs) stand-out for the removal of toxic heavy metals are viewed as an economically plausible and environmentally safe technique. GMMs are microorganisms whose genetic material has been changed utilizing genetic engineering techniques that exhibit enhanced removal efficiency in comparison with the other treatment methodologies. The present review comments the GMMs such as bacteria, algae and fungi and their potential for the removal of toxic heavy metals. This review provides current aspects of different advanced molecular tools which have been used to manipulate micro-organisms through genetic expression for the breakdown of metal compounds in polluted areas. The strategies, major limitations and challenges for genetic engineering of micro-organisms have been reviewed. The current review investigates the approaches working on utilizing genetically modified micro-organisms and effective removal techniques.
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Affiliation(s)
- A Saravanan
- Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
| | - B Ramesh
- Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - S Srinivasan
- Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
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Donassolo RA, Ferreira MRA, Moreira C, Dos Santos LM, Griep E, Moreira GMSG, Rodrigues RR, Moreira ÂN, Conceição FR. Formaldehyde effects on kanamycin resistance gene of inactivated recombinant Escherichia coli vaccines. Biotechnol Lett 2020; 42:2223-2230. [PMID: 32500473 DOI: 10.1007/s10529-020-02929-7] [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: 01/10/2020] [Accepted: 05/29/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Earlier studies have demonstrated the use of inactivated recombinant E. coli (bacterins), to protect against Clostridium spp. in vaccinated animals. These bacterins have a simpler, safer, and faster production process. However, these bacterins carry expression plasmids, containing antibiotic resistance gene, which could be assimilate accidentally by environmental microorganisms. Considering this, we aimed to impair this plasmids using formaldehyde at different concentrations. RESULTS This compound inactivated the highest density of cells in 24 h. KanR cassette amplification was found to be impaired with 0.8% for 24 h or 0.4% for 72 h. Upon electroporation, E. coli DH5α ultracompetent cells were unable to acquire the plasmids extracted from the bacterins after inactivation procedure. Formaldehyde-treated bacterins were incubated with other viable strains of E. coli, leading to no detectable gene transfer. CONCLUSIONS We found that this compound is effective as an inactivation agent. Here we demonstrate the biosafety involving antibiotic resistance gene of recombinant E. coli vaccines allowing to industrial production and animal application.
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Affiliation(s)
- Rafael A Donassolo
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil.
| | - Marcos Roberto A Ferreira
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil
| | - Clóvis Moreira
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil
| | - Lucas M Dos Santos
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil
| | - Emili Griep
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil
| | - Gustavo M S G Moreira
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie , Spielmannstr, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rafael R Rodrigues
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie , Spielmannstr, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ângela N Moreira
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil
| | - Fabricio R Conceição
- Centro de Desenvolvimento Tecnológico, Biotecnologia, Universidade Federal de Pelotas, Rio Grande do Sul, Pelotas, Brasil
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Metagenomic Insight Towards Vanillin-Mediated Membrane Biofouling Prevention: In Silico Docking Validation. Curr Microbiol 2020; 77:2233-2247. [PMID: 32382950 DOI: 10.1007/s00284-020-02003-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
Biofouling leads to water quality deterioration and higher maintenance cost for cleaning of membranes. The present study has demonstrated the application of a biomolecule (vanillin) in scrubbing and destabilizing biofilms of drinking water reverse osmosis (RO) membrane module in lab scale reactor set-up. Reverse osmosis membrane reactor was connected with tap water supply and subjected with optimal concentration of vanillin. The pressure drop was delayed by 17-20 days as compared to control reactor. Real-time PCR analysis of metagenome indicated the reduced copy number of functional biofilm-associated genes (bdlA, lasI, pgaC) in treated membrane. SEM and metagenome analysis revealed that the sticky biofilm communities shifted to loosely bound emboli after vanillin treatment. Metagenome sequence analysis revealed the inhibitory activity against major biofouling biota like members of Proteobacteria, Acidobacteria, Acnitobacteria, Bacteroidetes, Candidatus, Nitrospira, and Firmicutes. Biofouled membrane metagenome sequence was also compared with real-life (brackish water, waste water, domestic drinking water) biofouled membrane communities. In silico docking of vanillin to receptor proteins and chemical configuration simulation along with other phenolic derivatives were performed, which suggested that the autoiducer signal capability of vanillin was effective against representative broad spectrum biofilm population. Vanillin exhibited the quorum-quenching mode of action by virtue of docking towards similar amino acid (Thr 131, Ilu 214) responsible of autoinducer signal anchoring in the transcriptional regulatory proteins.
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Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. J Biol Eng 2018; 12:13. [PMID: 30123321 PMCID: PMC6090650 DOI: 10.1186/s13036-018-0105-8] [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: 01/17/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer. MAIN BODY Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system. CONCLUSION Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.
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Affiliation(s)
| | - Saskia Dymek
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Denise Kerkhoff
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Camilla März
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Olga Schmidt
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Maximilian Edich
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julian Droste
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Boas Pucker
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Present address: Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Christian Rückert
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0543-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Emerging technologies in bioremediation: constraints and opportunities. Biodegradation 2012; 23:917-26. [PMID: 22836784 DOI: 10.1007/s10532-012-9576-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/17/2012] [Indexed: 12/29/2022]
Abstract
Intensive industrialisation, inadequate disposal, large-scale manufacturing activities and leaks of organic compounds have resulted in long-term persistent sources of contamination of soil and groundwater. This is a major environmental, policy and health issue because of adverse effects of contaminants on humans and ecosystems. Current technologies for remediation of contaminated sites include chemical and physical remediation, incineration and bioremediation. With recent advancements, bioremediation offers an environmentally friendly, economically viable and socially acceptable option to remove contaminants from the environment. Three main approaches of bioremediation include use of microbes, plants and enzymatic remediation. All three approaches have been used with some success but are limited by various confounding factors. In this paper, we provide a brief overview on the approaches, their limitations and highlights emerging technologies that have potential to revolutionise the enzymatic and plant-based bioremediation approaches.
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Local adaptation of an introduced transgenic insect fungal pathogen due to new beneficial mutations. Proc Natl Acad Sci U S A 2011; 108:20449-54. [PMID: 22143757 DOI: 10.1073/pnas.1113824108] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Genetically modified Metarhizium spp represent a major new arsenal for combating insect pests and insect-borne diseases. However, for these tools to be used safely and effectively, we need a much better understanding of their evolutionary potential and invasion ecology. In order to model natural as well as anthropogenic dispersal scenarios, we investigated evolutionary processes in a green fluorescent protein tagged strain of Metarhizium robertsii following transfer from a semitropical to a temperate soil community. Adaptive changes occurred over four years despite recurrent genetic bottlenecks and lack of recombination with locally well adapted strains. By coupling microarray-based functional analysis with DNA hybridizations we determined that expression of cell wall and stress response genes evolved at an accelerated rate in multiple replicates, whereas virulence determinants, transposons, and chromosome structure were unaltered. The mutable genes were enriched for TATA boxes possibly because they are larger mutational targets. In further field trials, we showed that the new mutations increased the fitness of M. robertsii in the new range by enhancing saprophytic associations, and these benefits were maintained in subsequent years. Consistent with selection being habitat rather than host specific, populations of an avirulent mutant cycled with seasons similarly to the wild type, whereas a mutant unable to adhere to plant roots showed a linear decrease in population. Our results provide a mechanistic basis for understanding postrelease adaptations, show that agents can be selected that lack gene flow and virulence evolution, and describe a means of genetically containing transgenic strains by disrupting the Mad2 gene.
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Plakunov VK, Strelkova EA, Zhurina MV. Persistence and adaptive mutagenesis in biofilms. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710040028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Urgun-Demirtas M, Stark B, Pagilla K. Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants. Crit Rev Biotechnol 2008; 26:145-64. [PMID: 16923532 DOI: 10.1080/07388550600842794] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.
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Affiliation(s)
- Meltem Urgun-Demirtas
- Department of Chemical and Environmental Engineering, Illinois Institute of Technology, Chicago, 60616, USA
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Paul D, Pandey G, Pandey J, Jain RK. Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol 2005; 23:135-42. [PMID: 15734556 DOI: 10.1016/j.tibtech.2005.01.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biological methods for decontamination promise an improved substitute for ineffective and costly physico-chemical remediation methods, although so far only a fraction of the total microbial diversity (i.e. the culturable fraction with metabolic potential) has been harnessed for this purpose. Exploring and exploiting the "overlooked" genetic resource might ameliorate concerns associated with the degradation of recalcitrant and xenobiotic pollutants that are not degraded or only poorly degraded by known culturable bacteria. Recent advances in the molecular genetics of biodegradation and in knowledge-based methods of rational protein modification provide insight into the development of "designer biocatalysts" for environmental restoration. The application of such genetically engineered microorganisms (GEMs) in the environment has been limited, however, owing to the risks associated with uncontrolled growth and proliferation of the introduced biocatalyst and horizontal gene transfer. Programming rapid death of the biocatalyst soon after the depletion of the pollutant could minimize the risks in developing these technologies for successful bioremediation.
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Affiliation(s)
- Debarati Paul
- Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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Pandey G, Paul D, Jain RK. Conceptualizing “suicidal genetically engineered microorganisms” for bioremediation applications. Biochem Biophys Res Commun 2005; 327:637-9. [PMID: 15649393 DOI: 10.1016/j.bbrc.2004.12.080] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Indexed: 11/20/2022]
Abstract
Use of genetically modified microorganisms (GEMs) for pollution abatement has been limited because of risks associated with their release in the environment. Recent developments in the area of recombinant DNA technologies have paved the way for conceptualizing "suicidal genetically engineered microorganisms" (S-GEMS) to minimize such anticipated hazards and to achieve efficient and safer bioremediation of contaminated sites. Our strategy of designing a novel S-GEM is based on the knowledge of killer-anti-killer gene(s) that would be susceptible to programmed cell death after detoxification of any given contaminated site(s).
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Affiliation(s)
- Gunjan Pandey
- Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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Paul D, Pandey G, Jain RK. Suicidal genetically engineered microorganisms for bioremediation: Need and perspectives. Bioessays 2005; 27:563-73. [PMID: 15832375 DOI: 10.1002/bies.20220] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the past few decades, increased awareness of environmental pollution has led to the exploitation of microbial metabolic potential in the construction of several genetically engineered microorganisms (GEMs) for bioremediation purposes. At the same time, environmental concerns and regulatory constraints have limited the in situ application of GEMs, the ultimate objective behind their development. In order to address the anticipated risks due to the uncontrolled survival/dispersal of GEMs or recombinant plasmids into the environment, some attempts have been made to construct systems that would contain the released organisms. This article discusses the designing of safer genetically engineered organisms for environmental release with specific emphasis on the use of bacterial plasmid addiction systems to limit their survival thus minimizing the anticipated risk. We also conceptualize a novel strategy to construct "Suicidal Genetically Engineered Microorganisms (SGEMs)" by exploring/combining the knowledge of different plasmid addiction systems (such as antisense RNA-regulated plasmid addiction, proteic plasmid addiction etc.) and inducible degradative operons of bacteria.
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Affiliation(s)
- Debarati Paul
- Institute of Microbial Technology, Chandigarh, India
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Affiliation(s)
- M K Chattopadhyay
- Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
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