101
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Wagner HJ, Sprenger A, Rebmann B, Weber W. Upgrading biomaterials with synthetic biological modules for advanced medical applications. Adv Drug Deliv Rev 2016; 105:77-95. [PMID: 27179764 DOI: 10.1016/j.addr.2016.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/02/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
One key aspect of synthetic biology is the development and characterization of modular biological building blocks that can be assembled to construct integrated cell-based circuits performing computational functions. Likewise, the idea of extracting biological modules from the cellular context has led to the development of in vitro operating systems. This principle has attracted substantial interest to extend the repertoire of functional materials by connecting them with modules derived from synthetic biology. In this respect, synthetic biological switches and sensors, as well as biological targeting or structure modules, have been employed to upgrade functions of polymers and solid inorganic material. The resulting systems hold great promise for a variety of applications in diagnosis, tissue engineering, and drug delivery. This review reflects on the most recent developments and critically discusses challenges concerning in vivo functionality and tolerance that must be addressed to allow the future translation of such synthetic biology-upgraded materials from the bench to the bedside.
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102
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Eersels K, Lieberzeit P, Wagner P. A Review on Synthetic Receptors for Bioparticle Detection Created by Surface-Imprinting Techniques—From Principles to Applications. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00572] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kasper Eersels
- KU Leuven, Soft-Matter Physics and Biophysics
Section, Department of Physics and Astronomy, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Peter Lieberzeit
- University of Vienna, Faculty of Chemistry, Department
of Physical Chemistry, Währinger Straße 38, A-1090 Vienna, Austria
| | - Patrick Wagner
- KU Leuven, Soft-Matter Physics and Biophysics
Section, Department of Physics and Astronomy, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
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103
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Ueki T, Nevin KP, Woodard TL, Lovley DR. Genetic switches and related tools for controlling gene expression and electrical outputs of Geobacter sulfurreducens. J Ind Microbiol Biotechnol 2016; 43:1561-1575. [PMID: 27659960 DOI: 10.1007/s10295-016-1836-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/11/2016] [Indexed: 01/04/2023]
Abstract
Physiological studies and biotechnology applications of Geobacter species have been limited by a lack of genetic tools. Therefore, potential additional molecular strategies for controlling metabolism were explored. When the gene for citrate synthase, or acetyl-CoA transferase, was placed under the control of a LacI/IPTG regulator/inducer system, cells grew on acetate only in the presence of IPTG. The TetR/AT system could also be used to control citrate synthase gene expression and acetate metabolism. A strain that required IPTG for growth on D-lactate was constructed by placing the gene for D-lactate dehydrogenase under the control of the LacI/IPTG system. D-Lactate served as an inducer in a strain in which a D-lactate responsive promoter and transcription repressor were used to control citrate synthase expression. Iron- and potassium-responsive systems were successfully incorporated to regulate citrate synthase expression and growth on acetate. Linking the appropriate degradation tags on the citrate synthase protein made it possible to control acetate metabolism with either the endogenous ClpXP or exogenous Lon protease and tag system. The ability to control current output from Geobacter biofilms and the construction of an AND logic gate for acetate metabolism suggested that the tools developed may be applicable for biosensor and biocomputing applications.
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Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA.
| | - Kelly P Nevin
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Trevor L Woodard
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA
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104
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Del Vecchio D, Dy AJ, Qian Y. Control theory meets synthetic biology. J R Soc Interface 2016; 13:rsif.2016.0380. [PMID: 27440256 DOI: 10.1098/rsif.2016.0380] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022] Open
Abstract
The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology.
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Affiliation(s)
- Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron J Dy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yili Qian
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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105
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Comparative Analysis of UV Irradiation Effects on Escherichia coli and Pseudomonas aeruginosa Bacterial Cells Utilizing Biological and Computational Approaches. Cell Biochem Biophys 2016; 74:381-9. [DOI: 10.1007/s12013-016-0748-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/09/2016] [Indexed: 01/27/2023]
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106
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Kim HJ, Lim JW, Jeong H, Lee SJ, Lee DW, Kim T, Lee SJ. Development of a highly specific and sensitive cadmium and lead microbial biosensor using synthetic CadC-T7 genetic circuitry. Biosens Bioelectron 2016; 79:701-8. [DOI: 10.1016/j.bios.2015.12.101] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 12/08/2015] [Accepted: 12/29/2015] [Indexed: 10/22/2022]
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107
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Yung PY, Grasso LL, Mohidin AF, Acerbi E, Hinks J, Seviour T, Marsili E, Lauro FM. Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds. Sci Rep 2016; 6:19899. [PMID: 26818886 PMCID: PMC4730218 DOI: 10.1038/srep19899] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/21/2015] [Indexed: 12/16/2022] Open
Abstract
Volatile organic compounds (VOCs) are commonly used as solvents in various industrial settings. Many of them present a challenge to receiving environments, due to their toxicity and low bioavailability for degradation. Microorganisms are capable of sensing and responding to their surroundings and this makes them ideal detectors for toxic compounds. This study investigates the global transcriptomic responses of Escherichia coli K-12 to selected VOCs at sub-toxic levels. Cells grown in the presence of VOCs were harvested during exponential growth, followed by whole transcriptome shotgun sequencing (RNAseq). The analysis of the data revealed both shared and unique genetic responses compared to cells without exposure to VOCs. Results suggest that various functional gene categories, for example, those relating to Fe/S cluster biogenesis, oxidative stress responses and transport proteins, are responsive to selected VOCs in E. coli. The differential expression (DE) of genes was validated using GFP-promoter fusion assays. A variety of genes were differentially expressed even at non-inhibitory concentrations and when the cells are at their balanced-growth. Some of these genes belong to generic stress response and others could be specific to VOCs. Such candidate genes and their regulatory elements could be used as the basis for designing biosensors for selected VOCs.
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Affiliation(s)
- Pui Yi Yung
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Letizia Lo Grasso
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Abeed Fatima Mohidin
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Enzo Acerbi
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Enrico Marsili
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.,School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459.,School of Biotechnology, Dublin City University, Collins Avenue, Dublin 9, Ireland
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.,Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, N2-01C-45, Singapore 639798
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108
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Smith DG, Sajid N, Rehn S, Chandramohan R, Carney IJ, Khan MA, New EJ. A library-screening approach for developing a fluorescence sensing array for the detection of metal ions. Analyst 2016; 141:4608-13. [DOI: 10.1039/c6an00510a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A four-membered array based on fluorescent thiophenes is capable of distinguishing transition metal ions.
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Affiliation(s)
- David G. Smith
- School of Chemistry
- The University of Sydney
- NSW 2006
- Australia
| | - Naveed Sajid
- School of Chemistry
- The University of Sydney
- NSW 2006
- Australia
- Department of Chemistry
| | - Simone Rehn
- School of Chemistry
- The University of Sydney
- NSW 2006
- Australia
| | | | - Isaac J. Carney
- School of Chemistry
- The University of Sydney
- NSW 2006
- Australia
| | - Misbahul A. Khan
- Department of Chemistry
- The Islamia University of Bahawalpur
- Bahawalpur
- Pakistan
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109
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Progress in the biosensing techniques for trace-level heavy metals. Biotechnol Adv 2016; 34:47-60. [DOI: 10.1016/j.biotechadv.2015.12.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/21/2015] [Accepted: 12/02/2015] [Indexed: 01/08/2023]
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110
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Glasscock C, Lucks J, DeLisa M. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chem Biol 2016; 23:45-56. [DOI: 10.1016/j.chembiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022]
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111
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Application of genetically engineered microbial whole-cell biosensors for combined chemosensing. Appl Microbiol Biotechnol 2015; 100:1109-1119. [PMID: 26615397 DOI: 10.1007/s00253-015-7160-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 01/28/2023]
Abstract
The progress of genetically engineered microbial whole-cell biosensors for chemosensing and monitoring has been developed in the last 20 years. Those biosensors respond to target chemicals and produce output signals, which offer a simple and alternative way of assessment approaches. As actual pollution caused by human activities usually contains a combination of different chemical substances, how to employ those biosensors to accurately detect real contaminant samples and evaluate biological effects of the combined chemicals has become a realistic object of environmental researches. In this review, we outlined different types of the recent method of genetically engineered microbial whole-cell biosensors for combined chemical evaluation, epitomized their detection performance, threshold, specificity, and application progress that have been achieved up to now. We also discussed the applicability and limitations of this biosensor technology and analyzed the optimum conditions for their environmental assessment in a combined way.
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112
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Aracic S, Manna S, Petrovski S, Wiltshire JL, Mann G, Franks AE. Innovative biological approaches for monitoring and improving water quality. Front Microbiol 2015; 6:826. [PMID: 26322034 PMCID: PMC4532924 DOI: 10.3389/fmicb.2015.00826] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/27/2015] [Indexed: 12/20/2022] Open
Abstract
Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages.
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Affiliation(s)
- Sanja Aracic
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Sam Manna
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Steve Petrovski
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Jennifer L Wiltshire
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Gülay Mann
- Land Division, Defence Science and Technology Organisation , Melbourne, VIC, Australia
| | - Ashley E Franks
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
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113
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Synthetic biology expands chemical control of microorganisms. Curr Opin Chem Biol 2015; 28:20-8. [PMID: 26056951 DOI: 10.1016/j.cbpa.2015.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/30/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
Abstract
The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' responses to chemical stimuli resulting in the development of microbes as toxicity sensors, disease treatments, and chemical factories.
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114
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Bereza-Malcolm LT, Franks AE. Coupling anaerobic bacteria and microbial fuel cells as whole-cell environmental biosensors. MICROBIOLOGY AUSTRALIA 2015. [DOI: 10.1071/ma15045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Microorganisms have evolved to respond to environmental factors allowing adaption to changing conditions and minimisation of potential harm. Microbes have the ability to sense a wide range of biotic and abiotic factors including nutrient levels, analytes, temperature, contaminants, community quorum, and metabolic activity. Due to this ability, the use of whole-cell microbes as biosensors is attractive as it can provide real-time in situ information on biologically relevant factors through qualitative and quantitative outputs. Interestingly, many of the environments where these biosensors will be of most of use lack oxygen; and as such the use of anaerobic microorganisms to sense environmental factors with easy to use outputs is essential. Furthermore, sensing of contaminants can be linked with bioremediation of known contaminated environments, allowing a flexible, multiplexed device.
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