1
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Aulakh SK, Sellés Vidal L, South EJ, Peng H, Varma SJ, Herrera-Dominguez L, Ralser M, Ledesma-Amaro R. Spontaneously established syntrophic yeast communities improve bioproduction. Nat Chem Biol 2023:10.1038/s41589-023-01341-2. [PMID: 37248413 PMCID: PMC10374442 DOI: 10.1038/s41589-023-01341-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/14/2023] [Indexed: 05/31/2023]
Abstract
Nutritional codependence (syntrophy) has underexplored potential to improve biotechnological processes by using cooperating cell types. So far, design of yeast syntrophic communities has required extensive genetic manipulation, as the co-inoculation of most eukaryotic microbial auxotrophs does not result in cooperative growth. Here we employ high-throughput phenotypic screening to systematically test pairwise combinations of auxotrophic Saccharomyces cerevisiae deletion mutants. Although most coculture pairs do not enter syntrophic growth, we identify 49 pairs that spontaneously form syntrophic, synergistic communities. We characterized the stability and growth dynamics of nine cocultures and demonstrated that a pair of tryptophan auxotrophs grow by exchanging a pathway intermediate rather than end products. We then introduced a malonic semialdehyde biosynthesis pathway split between different pairs of auxotrophs, which resulted in increased production. Our results report the spontaneous formation of stable syntrophy in S. cerevisiae auxotrophs and illustrate the biotechnological potential of dividing labor in a cooperating intraspecies community.
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Affiliation(s)
- Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lara Sellés Vidal
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Eric J South
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Huadong Peng
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Sreejith Jayasree Varma
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucia Herrera-Dominguez
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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2
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Recent Progress in the Development of Droplet-based Microfluidic Technologies for Phenotypic Screening using Cell-cell Interactions. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Sharma B, Shukla P. Futuristic avenues of metabolic engineering techniques in bioremediation. Biotechnol Appl Biochem 2020; 69:51-60. [PMID: 33242354 DOI: 10.1002/bab.2080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/22/2020] [Indexed: 12/15/2022]
Abstract
Bioremediation is a promising technology for the treatment of environmental contaminants and paving new avenues for the betterment of the environment. Over the last some years, several approaches have been employed to optimize the genetic machinery of microorganisms relevant to bioremediation. Metabolic engineering is one of them that provides a new insight for bioremediation. This review envisages the critical role of these techniques toward exploring the possibilities of the creation of a new pathway, leading to pathway expansion to new substrates by assembling of catabolic modules from different origins in the same microbial cell. The recombinant DNA technology and gene editing tools were also explored for the construction of metabolically engineered microbial strains for the degradation of complex pollutants. Moreover, the importance of CRISPR-Cas system for knock-in and knock-out of genes was described by using recent studies. Further, the idea of the cocultivation of more than one metabolic engineered microbial communities is also discussed, which can be crucial in the bioremediation of multiple and complex pollutants. Finally, this review also elucidates the effective application of metabolic engineering in bioremediation through these techniques and tools.
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Affiliation(s)
- Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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4
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Lian S, Wu L, Nikolausz M, Lechtenfeld OJ, Richnow HH. 2H and 13C isotope fractionation analysis of organophosphorus compounds for characterizing transformation reactions in biogas slurry: Potential for anaerobic treatment of contaminated biomass. WATER RESEARCH 2019; 163:114882. [PMID: 31352241 DOI: 10.1016/j.watres.2019.114882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
The ability of anaerobic digestion (AD) to eliminate organophosphorus model compounds (OPs) with structural elements of phosphate, phosphorothioate and phosphorodithioate esters was studied. The enzymatic mechanism of the first irreversible degradation reaction was characterized using metabolite pattern and kinetic 2H/13C-isotope effect in original, cell-free and heat sterilized biogas slurry. The isotope fractionation study suggests different modes of degradation reactions. Representatives for phosphate ester, tris(2-chloroethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate, were hydrolyzed in biogas slurry without carbon or hydrogen isotope fractionation. Representatives for phosphorodithioate, Dimethoate and Malathion, were degraded in original slurry yielding carbon enrichment factor (εC) of -0.6 ± 0.1‰ and -5.5 ± 0.1‰ (-0.9 ± 0.1‰ and -7.2 ± 0.5‰ in cell-free slurry), without hydrogen isotope fractionation. Phosphorothioate degradation represented by Parathion and Parathion-methyl yielded surprisingly different εC (-0.7 ± 0.2 and -3.6 ± 0.4‰) and εH (-33 ± 5 and -5 ± 1‰) in original slurry compared to cell-free slurry (εC = -2.5 ± 0.5 and -8.6 ± 1.4‰; εH = -61 ± 10 and -10 ± 3‰) suggesting H-C bond cleavage. Degradation of Parathion and Parathion-methyl in sterilized slurry gave carbon but not hydrogen fractionation implying relative thermostable enzymatic activity with different mechanism. The correlation of 2H and 13C stable isotope fractionation of Parathion in biogas slurry showed distinct pattern (Λoriginal = 31 ± 11, Λcell-free = 20 ± 2), indicating different mechanism from chemical hydrolysis. Overall, AD can be a potential treatment for OPs contaminated biomass or contaminated organic waste material.
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Affiliation(s)
- Shujuan Lian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Langping Wu
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
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5
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Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC. Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci U S A 2019; 116:12804-12809. [PMID: 31186361 PMCID: PMC6600964 DOI: 10.1073/pnas.1900102116] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.
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Affiliation(s)
- Jared Kehe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anthony Kulesa
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anthony Ortiz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Sri Gowtham Thakku
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Health Sciences and Technology, MIT and Harvard, Cambridge, MA 02139
| | - Daniel Sellers
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155
| | - Seppe Kuehn
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel 76100
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
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6
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Guiziou S, Ulliana F, Moreau V, Leclere M, Bonnet J. An Automated Design Framework for Multicellular Recombinase Logic. ACS Synth Biol 2018; 7:1406-1412. [PMID: 29641183 PMCID: PMC5962929 DOI: 10.1021/acssynbio.8b00016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Tools
to systematically reprogram cellular behavior are crucial
to address pressing challenges in manufacturing, environment, or healthcare.
Recombinases can very efficiently encode Boolean and history-dependent
logic in many species, yet current designs are performed on a case-by-case
basis, limiting their scalability and requiring time-consuming optimization.
Here we present an automated workflow for designing recombinase logic
devices executing Boolean functions. Our theoretical framework uses
a reduced library of computational devices distributed into different
cellular subpopulations, which are then composed in various manners
to implement all desired logic functions at the multicellular level.
Our design platform called CALIN (Composable Asynchronous Logic using
Integrase Networks) is broadly accessible via a web
server, taking truth tables as inputs and providing corresponding
DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin). We anticipate that this automated design workflow will streamline
the implementation of Boolean functions in many organisms and for
various applications.
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Affiliation(s)
- Sarah Guiziou
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Federico Ulliana
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Violaine Moreau
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Michel Leclere
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
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7
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Free A, McDonald MA, Pagaling E. Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:131-189. [PMID: 30342721 DOI: 10.1016/bs.aambs.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.
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Affiliation(s)
- Andrew Free
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michael A McDonald
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Eulyn Pagaling
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
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8
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Zhang H, Wang X. Modular co-culture engineering, a new approach for metabolic engineering. Metab Eng 2016; 37:114-121. [PMID: 27242132 DOI: 10.1016/j.ymben.2016.05.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA.
| | - Xiaonan Wang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA
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9
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Ye H, Guo Z, Peng M, Cai C, Chen Y, Cao Y, Zhang W. Methyl Parathion Degrading Enzyme-based Nano-hybrid Biosensor for Enhanced Methyl Parathion Recognition. ELECTROANAL 2016. [DOI: 10.1002/elan.201501102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Haixia Ye
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education; Institute for Interdisciplinary Research; Jianghan University; Wuhan 430056 PR China
| | - Zhenzhong Guo
- School of Public Health, Medical College; Wuhan University of Science and Technology; Wuhan 430056 PR China
| | - Min Peng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education; Institute for Interdisciplinary Research; Jianghan University; Wuhan 430056 PR China
| | - Chunyan Cai
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education; Institute for Interdisciplinary Research; Jianghan University; Wuhan 430056 PR China
| | - Yong Chen
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education; Institute for Interdisciplinary Research; Jianghan University; Wuhan 430056 PR China
- Ecole Normale Supérieure; CNRS-ENS-UPMC UMR 8640; 24 Rue Lhomond Paris 75005 France
| | - Yiping Cao
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education; Institute for Interdisciplinary Research; Jianghan University; Wuhan 430056 PR China
| | - Weiying Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education; Institute for Interdisciplinary Research; Jianghan University; Wuhan 430056 PR China
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10
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Zomorrodi AR, Segrè D. Synthetic Ecology of Microbes: Mathematical Models and Applications. J Mol Biol 2015; 428:837-61. [PMID: 26522937 DOI: 10.1016/j.jmb.2015.10.019] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/17/2015] [Accepted: 10/21/2015] [Indexed: 12/29/2022]
Abstract
As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.
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Affiliation(s)
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA; Department of Biology, Boston University, Boston, MA; Department of Biomedical Engineering, Boston University, Boston, MA.
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11
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Artificial cell-cell communication as an emerging tool in synthetic biology applications. J Biol Eng 2015; 9:13. [PMID: 26265937 PMCID: PMC4531478 DOI: 10.1186/s13036-015-0011-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/25/2015] [Indexed: 01/14/2023] Open
Abstract
Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.
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12
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Li L, Zhang J, Lin J, Liu J. Biological technologies for the removal of sulfur containing compounds from waste streams: bioreactors and microbial characteristics. World J Microbiol Biotechnol 2015; 31:1501-15. [DOI: 10.1007/s11274-015-1915-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/30/2015] [Indexed: 11/24/2022]
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13
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Pan W, Zhang G, Zheng T, Wang P. Degradation of p-nitrophenol using CuO/Al2O3 as a Fenton-like catalyst under microwave irradiation. RSC Adv 2015. [DOI: 10.1039/c4ra14516j] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The CuO/Al2O3 was used as a heterogeneous catalyst for Fenton-like oxidation of PNP under microwave and the PNP removal was enhanced greatly by microwave.
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Affiliation(s)
- Weiqian Pan
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Guangshan Zhang
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Tong Zheng
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Peng Wang
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
- State Key Laboratory of Urban Water Resource and Environment
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14
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Biodegradation of hexachlorobenzene by a constructed microbial consortium. World J Microbiol Biotechnol 2014; 31:371-7. [DOI: 10.1007/s11274-014-1789-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
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15
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Jagmann N, Philipp B. Reprint of Design of synthetic microbial communities for biotechnological production processes. J Biotechnol 2014; 192 Pt B:293-301. [DOI: 10.1016/j.jbiotec.2014.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Jagmann N, Philipp B. Design of synthetic microbial communities for biotechnological production processes. J Biotechnol 2014; 184:209-18. [PMID: 24943116 DOI: 10.1016/j.jbiotec.2014.05.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/14/2014] [Accepted: 05/19/2014] [Indexed: 12/24/2022]
Abstract
In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes.
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Affiliation(s)
- Nina Jagmann
- Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, D-48149 Münster, Germany
| | - Bodo Philipp
- Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, D-48149 Münster, Germany.
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17
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Kim CS, Seo JH, Kang DG, Cha HJ. Engineered whole-cell biocatalyst-based detoxification and detection of neurotoxic organophosphate compounds. Biotechnol Adv 2014; 32:652-62. [DOI: 10.1016/j.biotechadv.2014.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/19/2014] [Accepted: 04/20/2014] [Indexed: 12/21/2022]
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18
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Xu S, Guo C, Li Y, Yu Z, Wei C, Tang Y. Methyl parathion imprinted polymer nanoshell coated on the magnetic nanocore for selective recognition and fast adsorption and separation in soils. JOURNAL OF HAZARDOUS MATERIALS 2014; 264:34-41. [PMID: 24275470 DOI: 10.1016/j.jhazmat.2013.10.060] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/01/2013] [Accepted: 10/28/2013] [Indexed: 06/02/2023]
Abstract
Core-shell magnetic methyl parathion (MP) imprinted polymers (Fe3O4@MPIPs) were fabricated by a layer-by-layer self-assembly process. In order to take full advantage of the synergistic effect of hydrogen-binding interactions and π-π accumulation between host and guest for molecular recognition, methacrylic acid and 4-vinyl pyridine were chosen as co-functional monomers and their optimal proportion were investigated. The core-shell and crystalline structure, morphology and magnetic properties of Fe3O4@MPIPs were characterized. The MP-imprinted nanoshell was almost uniform and about 100nm thick. Binding experiments demonstrated that Fe3O4@MPIPs possessed excellent binding properties, including high adsorption capacity and specific recognition, as well as fast adsorption kinetics and a fast phase separation rate. The equilibration adsorption capacity reached up to 9.1mg/g, which was 12 times higher than that of magnetic non-imprinted polymers, while adsorption reached equilibrium within 5min at a concentration of 0.2mmol/L. Furthermore, Fe3O4@MPIPs successfully provided selective separation and removal of MP in soils with a recovery and detection limit of 81.1-87.0% and 5.2ng/g, respectively.
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Affiliation(s)
- Shiying Xu
- School of Chemistry and Environment, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, China
| | - Changjuan Guo
- School of Chemistry and Environment, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, China
| | - Yongxian Li
- School of Chemistry and Environment, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, China
| | - Zerong Yu
- School of Chemistry and Environment, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, China
| | - Chaohai Wei
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, College of Environmental Science and Engineering, South China University of Technology, Guangzhou, China
| | - Youwen Tang
- School of Chemistry and Environment, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, China.
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Shong J, Jimenez Diaz MR, Collins CH. Towards synthetic microbial consortia for bioprocessing. Curr Opin Biotechnol 2012; 23:798-802. [PMID: 22387100 DOI: 10.1016/j.copbio.2012.02.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 02/10/2012] [Indexed: 10/28/2022]
Abstract
The use of microbial consortia for bioprocessing has been limited by our ability to reliably control community composition and function simultaneously. Recent advances in synthetic biology have enabled population-level coordination and control of ecosystem stability and dynamics. Further, new experimental and computational tools for screening and predicting community behavior have also been developed. The integration of synthetic biology with metabolic engineering at the community level is vital to our ability to apply system-level approaches to building and optimizing synthetic consortia for bioprocessing applications. This review details new methods, tools and opportunities that together have the potential to enable a new paradigm of bioprocessing using synthetic microbial consortia.
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Affiliation(s)
- Jasmine Shong
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180, USA
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Construction of a Genetically Engineered Microorganism that Simultaneously Degrades Organochlorine and Organophosphate Pesticides. Appl Biochem Biotechnol 2011; 166:590-8. [DOI: 10.1007/s12010-011-9450-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 11/02/2011] [Indexed: 11/25/2022]
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Characterization of a versatile rhizospheric organism from cucumber identified asOchrobactrum haematophilum. J Basic Microbiol 2011; 52:232-44. [DOI: 10.1002/jobm.201000491] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Accepted: 04/26/2011] [Indexed: 11/07/2022]
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Cotranslocation of methyl parathion hydrolase to the periplasm and of organophosphorus hydrolase to the cell surface of Escherichia coli by the Tat pathway and ice nucleation protein display system. Appl Environ Microbiol 2009; 76:434-40. [PMID: 19933341 DOI: 10.1128/aem.02162-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A genetically engineered Escherichia coli strain coexpressing organophosphorus hydrolase (OPH) and methyl parathion hydrolase (MPH) was constructed for the first time by cotransforming two compatible plasmids. Since these two enzymes have different substrate specificities, the coexpression strain showed a broader substrate range than strains expressing either one of the hydrolases. To reduce the mass transport limitation of organophosphates (OPs) across the cell membrane, MPH and OPH were simultaneously translocated to the periplasm and cell surface of E. coli, respectively, by employing the twin-arginine translocation (Tat) pathway and ice nucleation protein (INP) display system. The resulting recombinant strain showed sixfold-higher whole-cell activity than the control strain expressing cytosolic OP hydrolases. The correct localization of MPH and OPH was demonstrated by cell fractionation, immunoblotting, and enzyme activity assays. No growth inhibition was observed for the recombinant E. coli strain, and suspended cultures retained almost 100% of the activity over a period of 2 weeks. Owing to its high level of activity and superior stability, the recombinant E. coli strain could be employed as a whole-cell biocatalyst for detoxification of OPs. This strategy of utilizing dual translocation pathways should open up new avenues for cotranslocating multiple functional moieties to different extracytosolic compartments of a bacterial cell.
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