1
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Kumar A, Ponmani S, Sharma GK, Sangavi P, Chaturvedi AK, Singh A, Malyan SK, Kumar A, Khan SA, Shabnam AA, Jigyasu DK, Gull A. Plummeting toxic contaminates from water through phycoremediation: Mechanism, influencing factors and future outlook to enhance the capacity of living and non-living algae. ENVIRONMENTAL RESEARCH 2023; 239:117381. [PMID: 37832769 DOI: 10.1016/j.envres.2023.117381] [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: 05/03/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Freshwater habitats hold a unique role in the survival of all living organisms and supply water for drinking, irrigation, and life support activities. In recent decades, due to anthropogenic activities, deterioration in the water quality has been a long-lasting problem and challenge to the scientific fraternity. Although, these freshwater bodies have a bearable intrinsic capacity for pollution load however alarming increase in pollution limits the intrinsic capacities and requires additional technological interventions. The release of secondary pollutants from conventional interventions further needs revisiting the existing methodologies and asking for green interventions. Green interventions such as phycoremediation are natural, eco-friendly, economic, and energy-efficient alternatives and provide additional benefits such as nutrient recovery, biofuel production, and valuable secondary metabolites from polluted freshwater bodies. This systemic review in a nut-shell comprises the recent research insights on phycoremediation, technological implications, and influencing factors, and further discusses the associated mechanisms of metal ions biosorption by living and non-living algae, its advantages, and limitations. Besides, the article explores the possibility of future research prospects for applicability at a field scale that will help in the efficient utilization of resources, and improved ecological and health risks.
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Affiliation(s)
- A Kumar
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - S Ponmani
- Mother Terasa College of Agriculture, Tamil Nadu Agricultural University, Pudukkottai, 622 201, TN, India; Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute, Karaikudi, 630003, TN, India.
| | - G K Sharma
- ICAR-Indian Institute of Soil and Water Conservation, Research Centre, Dadwara Kota, 324002, Rajasthan, India.
| | - P Sangavi
- Mother Terasa College of Agriculture, Tamil Nadu Agricultural University, Pudukkottai, 622 201, TN, India; Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute, Karaikudi, 630003, TN, India.
| | - A K Chaturvedi
- Land and Water Management Research Group, Centre for Water Resources Development and Management, Kozhikode, Kerala, India.
| | - A Singh
- Department of Sustainable Energy Engineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
| | - S K Malyan
- Department of Environmental Studies, Dyal Singh Evening College, University of Delhi, New Delhi, 110003, India.
| | - A Kumar
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, 785000, India; Central Sericultural Research and Training Institute, Central Silk Board, Mysore, Karnataka, 570008, India.
| | - S A Khan
- Division of Environmental Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Aftab A Shabnam
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, 785000, India.
| | - D K Jigyasu
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, 785000, India.
| | - A Gull
- Central Sericultural Research and Training Institute, Central Silk Board, Mysore, Karnataka, 570008, India.
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2
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Pradhan B, Bhuyan PP, Nayak R, Patra S, Behera C, Ki JS, Ragusa A, Lukatkin AS, Jena M. Microalgal Phycoremediation: A Glimpse into a Sustainable Environment. TOXICS 2022; 10:toxics10090525. [PMID: 36136490 PMCID: PMC9502476 DOI: 10.3390/toxics10090525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 05/28/2023]
Abstract
Microalgae are continually exposed to heavy metals and metalloids (HMMs), which stifles their development and reproduction due to the resulting physiological and metabolic abnormalities, leading to lower crop productivity. They must thus change their way of adapting to survive in such a hostile environment without sacrificing their healthy growth, development, reproductive capacity, or survival. The mode of adaptation involves a complex relationship of signalling cascades that govern gene expression at the transcriptional and post-transcriptional levels, which consequently produces altered but adapted biochemical and physiochemical parameters. Algae have been reported to have altered their physicochemical and molecular perspectives as a result of exposure to a variety of HMMs. Hence, in this review, we focused on how microalgae alter their physicochemical and molecular characteristics as a tolerance mechanism in response to HMM-induced stress. Furthermore, physiological and biotechnological methods can be used to enhance extracellular absorption and clean up. The introduction of foreign DNA into microalgae cells and the genetic alteration of genes can boost the bio-accumulation and remediation capabilities of microalgae. In this regard, microalgae represent an excellent model organism and could be used for HMM removal in the near future.
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Affiliation(s)
- Biswajita Pradhan
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea
| | - Prajna Paramita Bhuyan
- Department of Botany, Maharaja Sriram Chandra Bhanja Deo University, Baripada 757003, Odisha, India
| | - Rabindra Nayak
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Srimanta Patra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769001, Odisha, India
| | - Chhandashree Behera
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea
| | - Andrea Ragusa
- CNR-Nanotec, Institute of Nanotechnology, Via Monteroni, 73100 Lecce, Italy
- Department of Biological and Environmental Sciences and Technologies, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Alexander S. Lukatkin
- Department of General Biology and Ecology, N.P. Ogarev Mordovia State University, Bolshevistskaja Str., 430005 Saransk, Russia
| | - Mrutyunjay Jena
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
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Abstract
The hypothesis presented here is that codes as described by Marcello Barbieri are the fundamental principle behind biological modularity. Modularity has been studied in different life science disciplines, especially in the fields of evolution and development, as well as in network biology, yet there is still no consensus on how modularity evolved itself. Modularity is basically the functional integrity of multiple molecular players involved in a common process. Codes as defined by Barbieri describe a tripartite relation involving an adapter molecule connecting two other independent types of molecules to each other in an arbitrary, but semantic manner. This form of interaction goes beyond predictable mere physical or chemical one-to-one interactions and always relates three molecules to each other. A code of three topologically related molecules interacting in a defined order may be considered a minimal module on its own, but when one regards a set of multiple, overlapping tripartite, coded interactions, this paves the way towards logically and functionally consistent coherence of multiple participants of a certain, modular process. A theoretical outline of how to identify and describe such modular structures is given.
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Danouche M, El Ghachtouli N, El Arroussi H. Phycoremediation mechanisms of heavy metals using living green microalgae: physicochemical and molecular approaches for enhancing selectivity and removal capacity. Heliyon 2021; 7:e07609. [PMID: 34355100 PMCID: PMC8322293 DOI: 10.1016/j.heliyon.2021.e07609] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/02/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Heavy metal (HM) contamination of water bodies is a serious global environmental problem. Because they are not biodegradable, they can accumulate in food chains, causing various signs of toxicity to exposed organisms, including humans. Due to its effectiveness, low cost, and ecological aspect, phycoremediation, or the use of microalgae's ecological functions in the treatment of HMs contaminated wastewater, is one of the most recommended processes. This study aims to examine in depth the mechanisms involved in the phycoremediation of HMs by microalgae, it also provides an overview of the prospects for improving the productivity, selectivity, and cost-effectiveness of this bioprocess through physicochemical and genetic engineering applications. Firstly, this review proposes a detailed examination of the biosorption interactions between cell wall functional groups and HMs, and their complexation with extracellular polymeric substances released by microalgae in the extracellular environment under stress conditions. Subsequently, the metal transporters involved in the intracellular bioaccumulation of HMs as well as the main intracellular mechanisms including compartmentalization in cell organelles, enzymatic biotransformation, or photoreduction of HMs were also extensively reviewed. In the last section, future perspectives of physicochemical and genetic approaches that could be used to improve the phytoremediation process in terms of removal efficiency, selectivity for a targeted metal, or reduction of treatment time and cost are discussed, which paves the way for large-scale application of phytoremediation processes.
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Affiliation(s)
- Mohammed Danouche
- Green Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco
- Microbial Biotechnology and Bioactive Molecules Laboratory, Sciences and Technologies Faculty, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Naïma El Ghachtouli
- Microbial Biotechnology and Bioactive Molecules Laboratory, Sciences and Technologies Faculty, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hicham El Arroussi
- Green Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco
- AgroBioScience (AgBS), Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
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5
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Design Methodologies and the Limits of the Engineering-Dominated Conception of Synthetic Biology. Acta Biotheor 2019; 67:1-18. [PMID: 30121875 DOI: 10.1007/s10441-018-9338-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 08/14/2018] [Indexed: 10/28/2022]
Abstract
Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational design and directed evolution. Rational design resembles the design methodology of traditional engineering sciences. However, it is often replaced and complemented by the more biologically-inspired method of directed evolution, which models itself on natural evolution. These two approaches take philosophically different stances to the design of biological systems. Rational design aims to make biological systems more machine-like, whereas directed evolution utilizes variation and emergent features of living systems. I provide an analysis of the methodological basis of these design approaches, and highlight important methodological differences between them. By analyzing the respective benefits and limitations of these approaches, I argue against the engineering-dominated conception of synthetic biology and its "methodological monism", where the rational design approach is taken as the default design methodology. Alternative design methodologies, like directed evolution, should be considered as complementary, not competitive, to rational design.
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6
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Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation. Genes (Basel) 2018; 10:genes10010017. [PMID: 30597824 PMCID: PMC6356944 DOI: 10.3390/genes10010017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 02/08/2023] Open
Abstract
The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. Here, we present the strategies that have been utilized to fundamentally alter the genetic code in its decoding rules or its molecular representation and anticipate future avenues in the pursuit of robust biocontainment.
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7
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Schmidt M, Pei L, Budisa N. Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:301-315. [PMID: 28567486 DOI: 10.1007/10_2016_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.
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Affiliation(s)
- Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria.
| | - Lei Pei
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria
| | - Nediljko Budisa
- AK Biokatalyse, Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
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8
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Bardaji L, Añorga M, Ruiz-Masó JA, Del Solar G, Murillo J. Plasmid Replicons from Pseudomonas Are Natural Chimeras of Functional, Exchangeable Modules. Front Microbiol 2017; 8:190. [PMID: 28243228 PMCID: PMC5304414 DOI: 10.3389/fmicb.2017.00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/25/2017] [Indexed: 01/05/2023] Open
Abstract
Plasmids are a main factor for the evolution of bacteria through horizontal gene exchange, including the dissemination of pathogenicity genes, resistance to antibiotics and degradation of pollutants. Their capacity to duplicate is dependent on their replication determinants (replicon), which also define their bacterial host range and the inability to coexist with related replicons. We characterize a second replicon from the virulence plasmid pPsv48C, from Pseudomonas syringae pv. savastanoi, which appears to be a natural chimera between the gene encoding a newly described replication protein and a putative replication control region present in the widespread family of PFP virulence plasmids. We present extensive evidence of this type of chimerism in structurally similar replicons from species of Pseudomonas, including environmental bacteria as well as plant, animal and human pathogens. We establish that these replicons consist of two functional modules corresponding to putative control (REx-C module) and replication (REx-R module) regions. These modules are functionally separable, do not show specificity for each other, and are dynamically exchanged among replicons of four distinct plasmid families. Only the REx-C module displays strong incompatibility, which is overcome by a few nucleotide changes clustered in a stem-and-loop structure of a putative antisense RNA. Additionally, a REx-C module from pPsv48C conferred replication ability to a non-replicative chromosomal DNA region containing features associated to replicons. Thus, the organization of plasmid replicons as independent and exchangeable functional modules is likely facilitating rapid replicon evolution, fostering their diversification and survival, besides allowing the potential co-option of appropriate genes into novel replicons and the artificial construction of new replicon specificities.
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Affiliation(s)
- Leire Bardaji
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra Pamplona, Spain
| | - Maite Añorga
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra Pamplona, Spain
| | - José A Ruiz-Masó
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Gloria Del Solar
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Jesús Murillo
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra Pamplona, Spain
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9
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Mısırlı G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A. Data Integration and Mining for Synthetic Biology Design. ACS Synth Biol 2016; 5:1086-1097. [PMID: 27110921 DOI: 10.1021/acssynbio.5b00295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.
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Affiliation(s)
- Göksel Mısırlı
- School
of Computing Science, Newcastle University, NE1 7RU Newcastle
upon Tyne, United Kingdom
| | - Jennifer Hallinan
- School
of Computing Science, Newcastle University, NE1 7RU Newcastle
upon Tyne, United Kingdom
| | - Matthew Pocock
- School
of Computing Science, Newcastle University, NE1 7RU Newcastle
upon Tyne, United Kingdom
- Turing Ate My Hamster Ltd, NE27
0RT Newcastle upon Tyne, United Kingdom
| | - Phillip Lord
- School
of Computing Science, Newcastle University, NE1 7RU Newcastle
upon Tyne, United Kingdom
| | | | - Herbert Sauro
- Department
of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Anil Wipat
- School
of Computing Science, Newcastle University, NE1 7RU Newcastle
upon Tyne, United Kingdom
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10
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Zeraatkar AK, Ahmadzadeh H, Talebi AF, Moheimani NR, McHenry MP. Potential use of algae for heavy metal bioremediation, a critical review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 181:817-831. [PMID: 27397844 DOI: 10.1016/j.jenvman.2016.06.059] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/11/2016] [Accepted: 06/26/2016] [Indexed: 05/11/2023]
Abstract
Algae have several industrial applications that can lower the cost of biofuel co-production. Among these co-production applications, environmental and wastewater bioremediation are increasingly important. Heavy metal pollution and its implications for public health and the environment have led to increased interest in developing environmental biotechnology approaches. We review the potential for algal biosorption and/or neutralization of the toxic effects of heavy metal ions, primarily focusing on their cellular structure, pretreatment, modification, as well as potential application of genetic engineering in biosorption performance. We evaluate pretreatment, immobilization, and factors affecting biosorption capacity, such as initial metal ion concentration, biomass concentration, initial pH, time, temperature, and interference of multi metal ions and introduce molecular tools to develop engineered algal strains with higher biosorption capacity and selectivity. We conclude that consideration of these parameters can lead to the development of low-cost micro and macroalgae cultivation with high bioremediation potential.
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Affiliation(s)
| | - Hossein Ahmadzadeh
- Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, 1436-91779, Iran.
| | - Ahmad Farhad Talebi
- Genetic Department, Faculty of Biotechnology, Semnan University, Semnan, 35131-19111, Iran
| | - Navid R Moheimani
- Algae R&D Centre, School of Veterinary and Life Sciences, Murdoch University, Australia
| | - Mark P McHenry
- School of Engineering and Information Technology, Murdoch University, Australia
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11
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Ollé-Vila A, Duran-Nebreda S, Conde-Pueyo N, Montañez R, Solé R. A morphospace for synthetic organs and organoids: the possible and the actual. Integr Biol (Camb) 2016; 8:485-503. [PMID: 27032985 DOI: 10.1039/c5ib00324e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.
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Affiliation(s)
- Aina Ollé-Vila
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
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12
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Wang Z, Wu X, Peng J, Hu Y, Fang B, Huang S. Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density. PLoS One 2014; 9:e104578. [PMID: 25119347 PMCID: PMC4132116 DOI: 10.1371/journal.pone.0104578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 07/15/2014] [Indexed: 01/31/2023] Open
Abstract
Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell–cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model.
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Affiliation(s)
- Zhaoshou Wang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Xin Wu
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Jianghai Peng
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yidan Hu
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Baishan Fang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Chemical Biology of Fujian Province, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
- * E-mail:
| | - Shiyang Huang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
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13
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Ye H, Fussenegger M. Synthetic therapeutic gene circuits in mammalian cells. FEBS Lett 2014; 588:2537-44. [PMID: 24844435 DOI: 10.1016/j.febslet.2014.05.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/05/2014] [Indexed: 12/19/2022]
Abstract
In the emerging field of synthetic biology, scientists are focusing on designing and creating functional devices, systems, and organisms with novel functions by engineering and assembling standardised biological building blocks. The progress of synthetic biology has significantly advanced the design of functional gene networks that can reprogram metabolic activities in mammalian cells and provide new therapeutic opportunities for future gene- and cell-based therapies. In this review, we describe the most recent advances in synthetic mammalian gene networks designed for biomedical applications, including how these synthetic therapeutic gene circuits can be assembled to control signalling networks and applied to treat metabolic disorders, cancer, and immune diseases. We conclude by discussing the various challenges and future prospects of using synthetic mammalian gene networks for disease therapy.
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Affiliation(s)
- Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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14
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15
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Ying BW, Tsuru S, Seno S, Matsuda H, Yomo T. Gene expression scaled by distance to the genome replication site. MOLECULAR BIOSYSTEMS 2013; 10:375-9. [PMID: 24336896 DOI: 10.1039/c3mb70254e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A simple mode of gene expression scaled by the distance from the chromosomal location of the gene to the genome replication site oriC was determined. The common formula representing the effect of genomic position on expression capacity not only supports the multifork replication model but also provides a base correlation for theoretical simulation and synthetic constructs.
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Affiliation(s)
- Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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16
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Dharmadi Y, Patel K, Shapland E, Hollis D, Slaby T, Klinkner N, Dean J, Chandran SS. High-throughput, cost-effective verification of structural DNA assembly. Nucleic Acids Res 2013; 42:e22. [PMID: 24203706 PMCID: PMC3936733 DOI: 10.1093/nar/gkt1088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA ‘assembly’ from ‘building blocks’ remains a cornerstone in synthetic biology, whether it be for gene synthesis (∼1 kb), pathway engineering (∼10 kb) or synthetic genomes (>100 kb). Despite numerous advances in the techniques used for DNA assembly, verification of the assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at <$1 per sample.
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Affiliation(s)
- Yandi Dharmadi
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
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17
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18
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Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. Tuning response curves for synthetic biology. ACS Synth Biol 2013; 2:547-67. [PMID: 23905721 PMCID: PMC3805330 DOI: 10.1021/sb4000564] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/07/2023]
Abstract
Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system's dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.
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Affiliation(s)
- Jordan Ang
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Edouard Harris
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Brendan J. Hussey
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Richard Kil
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - David R. McMillen
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
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19
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Trosset JY, Carbonell P. Synergistic Synthetic Biology: Units in Concert. Front Bioeng Biotechnol 2013; 1:11. [PMID: 25022769 PMCID: PMC4090895 DOI: 10.3389/fbioe.2013.00011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/01/2013] [Indexed: 01/31/2023] Open
Abstract
Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.
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Affiliation(s)
| | - Pablo Carbonell
- BioRetroSynth Laboratory, Institute of Systems and Synthetic Biology, University of Evry-Val d'Essonne , Evry , France ; BioRetroSynth Laboratory, Institute of Systems and Synthetic Biology, CNRS , Evry , France
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20
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Heng BC, Aubel D, Fussenegger M. G protein-coupled receptors revisited: therapeutic applications inspired by synthetic biology. Annu Rev Pharmacol Toxicol 2013; 54:227-49. [PMID: 24160705 DOI: 10.1146/annurev-pharmtox-011613-135921] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to hormones and neurotransmitters within the human body. They have much potential in the emerging field of synthetic biology, which is the rational, systematic design of biological systems with desired functionality. The responsiveness of GPCRs to a plethora of endogenous and exogenous ligands and stimuli make them ideal sensory receptor modules of synthetic gene networks. Such networks can activate target gene expression in response to a specific stimulus. Additionally, because GPCRs are important pharmacological targets of various human diseases, genes encoding their protein/peptide ligands can also be incorporated as target genes of the response output elements of synthetic gene networks. This review aims to critically examine the potential role of GPCRs in constructing therapeutic synthetic gene networks and to discuss various challenges in utilizing GPCRs for synthetic biology applications.
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Affiliation(s)
- Boon Chin Heng
- Department of Biosystems Science and Engineering, ETH Zürich, CH-4058 Basel, Switzerland;
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21
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Calvert J. Engineering Biology and Society: Reflections on Synthetic Biology. SCIENCE TECHNOLOGY AND SOCIETY 2013. [DOI: 10.1177/0971721813498501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Synthetic biology, according to some definitions, is the attempt to make biology into an engineering discipline. I ask what is meant by this objective, which seems to have excited and energised many people and encouraged them to start working in the field. I show how synthetic biologists make a point of distinguishing their work from previous genetic ‘engineering’, which is described as bespoke and artisan. I examine synthetic biologists’ accounts of the differences between biology and engineering, which often oppose comprehension to construction. I argue that synthetic biology, like other branches of engineering, aims to meet recognised needs, and to make the world more manipulable and controllable. But there are tensions within the field—some synthetic biologists have reservations about the extent to which biology can be engineered, and ask whether it is necessary to develop a new type of engineering when working with living systems. After exploring these debates, I turn to some of the broader consequences of making biology easier to engineer, particularly the deskilling and democratisation of the technology. I end by arguing that because synthetic biologists are skilled at bringing together both technical and social forces, they are appropriately described as ‘heterogeneous engineers’.
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Affiliation(s)
- Jane Calvert
- Jane Calvert, Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons’ Hall, Edinburgh, EH1 1LZ, UK
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22
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Gregorio-Godoy P, Míguez DG. Synthetic approaches to study transcriptional networks and noise in mammalian systems. IET Syst Biol 2013; 7:11-7. [PMID: 23848051 DOI: 10.1049/iet-syb.2012.0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synthetic biology aims to build new functional organisms and to rationally re-design existing ones by applying the engineering principle of modularity. Apart from building new life forms to perform technical applications, the approach of synthetic biology is useful to dissect complex biological phenomena into simple and easy to understand synthetic modules. Synthetic gene networks have been successfully implemented in prokaryotes and lower eukaryotes, with recent approaches moving ahead towards the mammalian environment. However, synthetic circuits in higher eukaryotes present a more challenging scenario, since its reliability is compromised because of the strong stochastic nature of transcription. Here, the authors review recent approaches that take advantage of the noisy response of synthetic regulatory circuits to learn key features of the complex machinery that orchestrates transcription in higher eukaryotes. Understanding the causes and consequences of biological noise will allow us to design more reliable mammalian synthetic circuits with revolutionary medical applications.
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Affiliation(s)
- Paula Gregorio-Godoy
- Facultad de Ciencias, Departamento de Física de la Materia Condensada e Instituto Nicolás Cabrera, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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23
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Purcell O, Jain B, Karr JR, Covert MW, Lu TK. Towards a whole-cell modeling approach for synthetic biology. CHAOS (WOODBURY, N.Y.) 2013; 23:025112. [PMID: 23822510 PMCID: PMC3695969 DOI: 10.1063/1.4811182] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole-cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline.
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Affiliation(s)
- Oliver Purcell
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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24
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Qi H, Blanchard A, Lu T. Engineered genetic information processing circuits. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:273-87. [DOI: 10.1002/wsbm.1216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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25
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Design and Application of Synthetic Biology Devices for Therapy. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Lamsen EN, Atsumi S. Recent progress in synthetic biology for microbial production of C3-C10 alcohols. Front Microbiol 2012; 3:196. [PMID: 22701113 PMCID: PMC3370425 DOI: 10.3389/fmicb.2012.00196] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/14/2012] [Indexed: 01/17/2023] Open
Abstract
The growing need to address current energy and environmental problems has sparked an interest in developing improved biological methods to produce liquid fuels from renewable sources. While microbial ethanol production is well established, higher-chain alcohols possess chemical properties that are more similar to gasoline. Unfortunately, these alcohols (except 1-butanol) are not produced efficiently in natural microorganisms, and thus economical production in industrial volumes remains a challenge. Synthetic biology, however, offers additional tools to engineer synthetic pathways in user-friendly hosts to help increase titers and productivity of these advanced biofuels. This review concentrates on recent developments in synthetic biology to produce higher-chain alcohols as viable renewable replacements for traditional fuel.
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Affiliation(s)
- Edna N Lamsen
- Department of Chemistry, University of California, Davis, CA, USA
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27
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Gardner L, Deiters A. Light-controlled synthetic gene circuits. Curr Opin Chem Biol 2012; 16:292-9. [PMID: 22633822 DOI: 10.1016/j.cbpa.2012.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 04/10/2012] [Accepted: 04/15/2012] [Indexed: 01/09/2023]
Abstract
Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.
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Affiliation(s)
- Laura Gardner
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, United States
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28
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Synthetic Biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production. FEBS Lett 2012; 586:2171-6. [DOI: 10.1016/j.febslet.2012.04.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/13/2012] [Accepted: 04/13/2012] [Indexed: 01/12/2023]
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Abstract
One important aim of synthetic biology is to develop a self-replicating biological system capable of performing useful tasks. A mathematical model of a synthetic organism would greatly enhance its value by providing a platform in which proposed modifications to the system could be rapidly prototyped and tested. Such a platform would allow the explicit connection of genomic sequence information to physiological predictions. As an initial step toward this aim, a minimal cell model (MCM) has been formulated. The MCM is defined as a model of a hypothetical cell with the minimum number of genes necessary to grow and divide in an optimally supportive culture environment. It is chemically detailed in terms of genes and gene products, as well as physiologically complete in terms of bacterial cell processes (e.g., DNA replication and cell division). A mathematical framework originally developed for modeling Escherichia coli has been used to build the platform MCM. A MCM with 241 product-coding genes (those which produce protein or stable RNA products) is presented. This gene set is genomically complete in that it codes for all the functions that a minimal chemoheterotrophic bacterium would require for sustained growth and division. With this model, the hypotheses behind a minimal gene set can be tested using a chemically detailed, dynamic, whole-cell modeling approach. Furthermore, the MCM can simulate the behavior of a whole cell that depends on the cell's (1) metabolic rates and chemical state, (2) genome in terms of expression of various genes, (3) environment both in terms of direct nutrient starvation and competitive inhibition leading to starvation, and (4) genomic sequence in terms of the chromosomal locations of genes.
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Affiliation(s)
- Michael L Shuler
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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30
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Wang J, Xiong Z, Meng H, Wang Y, Wang Y. Synthetic biology triggers new era of antibiotics development. Subcell Biochem 2012; 64:95-114. [PMID: 23080247 DOI: 10.1007/978-94-007-5055-5_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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Abstract
Synthetic biology aims to create functional devices, systems and organisms with novel and useful functions on the basis of catalogued and standardized biological building blocks. Although they were initially constructed to elucidate the dynamics of simple processes, designed devices now contribute to the understanding of disease mechanisms, provide novel diagnostic tools, enable economic production of therapeutics and allow the design of novel strategies for the treatment of cancer, immune diseases and metabolic disorders, such as diabetes and gout, as well as a range of infectious diseases. In this Review, we cover the impact and potential of synthetic biology for biomedical applications.
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Affiliation(s)
- Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, D-79104 Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Hebelstrasse 25, Freiburg, D-79104 Germany
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058 Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, Basel, CH-4058 Switzerland
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32
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Boyle PM, Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng 2011; 14:223-32. [PMID: 22037345 DOI: 10.1016/j.ymben.2011.10.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/05/2011] [Accepted: 10/16/2011] [Indexed: 11/24/2022]
Abstract
Synthetic biologists combine modular biological "parts" to create higher-order devices. Metabolic engineers construct biological "pipes" by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design.
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Affiliation(s)
- Patrick M Boyle
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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33
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Gardner L, Zou Y, Mara A, Cropp TA, Deiters A. Photochemical control of bacterial signal processing using a light-activated erythromycin. MOLECULAR BIOSYSTEMS 2011; 7:2554-7. [PMID: 21785768 DOI: 10.1039/c1mb05166k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial cells control resistance to the macrolide antibiotic erythromycin using the MphR(A) repressor protein. Erythromycin binds to MphR(A), causing release of the PmphR promoter, activating expression of the 2'-phosphotransferase Mph(A). We engineered the MphR(A)/promoter system to, in conjunction with a light-activatable derivative of erythromycin, enable photochemical activation of gene expression in E. coli. We applied this photochemical gene switch to the construction of a light-triggered logic gate, a light-controlled band-pass filter, as well as spatial and temporal control of gene expression.
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Affiliation(s)
- Laura Gardner
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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34
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Chavali S, Morais DADL, Gough J, Babu MM. Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica. Bioessays 2011; 33:592-601. [DOI: 10.1002/bies.201100034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Salvado B, Karathia H, Chimenos AU, Vilaprinyo E, Omholt S, Sorribas A, Alves R. Methods for and results from the study of design principles in molecular systems. Math Biosci 2011; 231:3-18. [DOI: 10.1016/j.mbs.2011.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 01/24/2011] [Accepted: 02/10/2011] [Indexed: 12/27/2022]
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36
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Krivoruchko A, Siewers V, Nielsen J. Opportunities for yeast metabolic engineering: Lessons from synthetic biology. Biotechnol J 2011; 6:262-76. [DOI: 10.1002/biot.201000308] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 01/06/2011] [Accepted: 01/13/2011] [Indexed: 11/08/2022]
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37
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Nelson JW, Chamessian AG, McEnaney PJ, Murelli RP, Kazmiercak BI, Spiegel DA, Spiegel DA. A biosynthetic strategy for re-engineering the Staphylococcus aureus cell wall with non-native small molecules. ACS Chem Biol 2010; 5:1147-55. [PMID: 20923200 DOI: 10.1021/cb100195d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Staphylococcus aureus (S. aureus) is a Gram-positive bacterial pathogen that has emerged as a major public health threat. Here we report that the cell wall of S. aureus can be covalently re-engineered to contain non-native small molecules. This process makes use of endogenous levels of the bacterial enzyme sortase A (SrtA), which ordinarily functions to incorporate proteins into the bacterial cell wall. Thus, incubation of wild-type bacteria with rationally designed SrtA substrates results in covalent incorporation of functional molecular handles (fluorescein, biotin, and azide) into cell wall peptidoglycan. These conclusions are supported by data obtained through a variety of experimental techniques (epifluorescence and electron microscopy, biochemical extraction, and mass spectrometry), and cell-wall-incorporated azide was exploited as a chemical handle to perform an azide-alkyne cycloaddition reaction on the bacterial cell surface. This report represents the first example of cell wall engineering of S. aureus or any other pathogenic Gram-positive bacteria and has the potential for widespread utility.
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Affiliation(s)
- James W. Nelson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
| | | | | | - Ryan P. Murelli
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
| | - Barbara I. Kazmiercak
- Department of Medicine (Infectious Diseases), Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06520
| | - David A. Spiegel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
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38
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Gao H, Zhuo Y, Ashforth E, Zhang L. Engineering of a genome-reduced host: practical application of synthetic biology in the overproduction of desired secondary metabolites. Protein Cell 2010; 1:621-6. [PMID: 21203934 DOI: 10.1007/s13238-010-0073-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 05/28/2010] [Indexed: 12/23/2022] Open
Abstract
Synthetic biology aims to design and build new biological systems with desirable properties, providing the foundation for the biosynthesis of secondary metabolites. The most prominent representation of synthetic biology has been used in microbial engineering by recombinant DNA technology. However, there are advantages of using a deleted host, and therefore an increasing number of biotechnology studies follow similar strategies to dissect cellular networks and construct genome-reduced microbes. This review will give an overview of the strategies used for constructing and engineering reduced-genome factories by synthetic biology to improve production of secondary metabolites.
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Affiliation(s)
- Hong Gao
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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39
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40
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Foley PL, Shuler ML. Considerations for the design and construction of a synthetic platform cell for biotechnological applications. Biotechnol Bioeng 2010; 105:26-36. [PMID: 19816966 DOI: 10.1002/bit.22575] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The design and construction of an artificial bacterial cell could revolutionize biotechnological processes and technologies. A functional platform cell that can be easily customized for a pre-defined task would be useful for applications from producing therapeutics to decontaminating waste streams. The platform cell must be robust and highly efficient. A biotechnological platform cell is related to the concept of a minimal cell, but several factors beyond those necessary for a minimal cell must be considered for a synthetic organism designed for biotechnological applications. Namely, a platform cell must exhibit robust cell reproduction, decreased genetic drift, a physically robust cell envelope, efficient and simplified transcription and translation controls, and predictable metabolic interactions. Achieving a biotechnological platform cell will benefit from insights acquired from a minimal cell, but an approach of minimizing an existing organism's genome may be a more practical experimental approach. Escherichia coli possess many of the desired characteristics of a platform cell and could serve as a useful model organism for the design and construction of a synthetic platform organism. In this article we review briefly the current state of research in this field and outline specific characteristics that will be important for a biotechnologically relevant synthetic cell that has a minimized genome and efficient regulatory structure.
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Affiliation(s)
- P L Foley
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
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Afonso B, Silver PA, Ajo-Franklin CM. A synthetic circuit for selectively arresting daughter cells to create aging populations. Nucleic Acids Res 2010; 38:2727-35. [PMID: 20150416 PMCID: PMC2860115 DOI: 10.1093/nar/gkq075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The ability to engineer genetic programs governing cell fate will permit new safeguards for engineered organisms and will further the biological understanding of differentiation and aging. Here, we have designed, built and implemented a genetic device in the budding yeast Saccharomyces cerevisiae that controls cell-cycle progression selectively in daughter cells. The synthetic device was built in a modular fashion by combining timing elements that are coupled to the cell cycle, i.e. cell-cycle specific promoters and protein degradation domains, and an enzymatic domain which conditionally confers cell arrest. Thus, in the presence of a drug, the device is designed to arrest growth of only newly-divided daughter cells in the population. Indeed, while the engineered cells grow normally in the absence of drug, with the drug the engineered cells display reduced, linear growth on the population level. Fluorescence microscopy of single cells shows that the device induces cell arrest exclusively in daughter cells and radically shifts the age distribution of the resulting population towards older cells. This device, termed the ‘daughter arrester’, provides a blueprint for more advanced devices that mimic developmental processes by having control over cell growth and death.
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Affiliation(s)
- Bruno Afonso
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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