Synthetic biology: new engineering rules for an emerging discipline (original) (raw)
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The second wave of synthetic biology: from modules to systems
Nature Reviews Molecular Cell Biology, 2009
Synthetic biology has the potential to transform how we interact with our environment and how we approach human health. Conventional genetic engineering approaches for solving complex problems typically focus on tweaking one or a few genes. Synthetic biology, by contrast, approaches these problems from a novel, engineering-driven perspective that focuses on wholesale changes to existing cellular architectures and the construction of elaborate systems from the ground up. Synthetic biology has the potential to fabricate practical organisms that could clean hazardous waste in inaccessible places 1 , to use plants to sense chemicals and respond accordingly 2,3 , to produce clean fuel in an efficient and sustainable fashion 4 , or to recognize and destroy tumours 5 . Whether addressing an existing problem or creating new capabilities, effective solutions can be inspired by, but need not mimic, natural biological processes. Our new designs can potentially be more robust or efficient than systems that have been fashioned by evolution.
Synthetic Biology: A Bridge between Artificial and Natural Cells
Life (Basel, Switzerland), 2014
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artifi...
Synthetic biology - putting engineering into biology
Bioinformatics/computer Applications in The Biosciences, 2006
Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization, and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating, or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis -synthetic biology's system fabrication process -supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.
A Perspective of Synthetic Biology: Assembling building blocks for novel functions
Synthetic biology is a recently emerging field that applies engineering formalisms to design and construct new biological parts, devices, and systems for novel functions or life forms that do not exist in nature. Synthetic biology relies on and shares tools from genetic engineering, bioengineering, systems biology and many other engineering disciplines. It is also different from these subjects, in both insights and approach. Applications of synthetic biology have great potential for novel contributions to established fields and for offering opportunities to answer fundamentally new biological questions. This article does not aim at a thorough survey of the literature and detailing progress in all different directions. Instead, it is intended to communicate a way of thinking for synthetic biology in which basic functional elements are defined and assembled into living systems or biomaterials with new properties and behaviors. Four major application areas with a common theme are discussed and a procedure (or “protocol”) for a standard synthetic biology work is suggested.
Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes
Journal of Biomedicine and Biotechnology, 2010
The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of int...
The Emerging Field of Synthetic Biology: a Review
2012
Synthetic biology which is concerned with engineering organisms to perform novel functions and developing the ways by which organisms can be engineered easily and robustly, is a relatively young field with a large potential for growth. Much of the work in the field involves design and construction of genetic circuitry, the piecing together of biological "parts", such as promoters and ribosome binding sites, to form the basis for biological "devices" which are organisms that have an engineered, well-specified input-output behavior. The idea in synthetic biology is applying engineering principles, such as hierarchical design, modular reusable parts and standard interfaces to construct bio-systems. The results of these engineering efforts can be of great value to human interests such as medicine and industry. In this paper first some related terms and resources for synthetic biology are described. Then existing computational tools and methods for synthetic biology are explored. It is followed by a discussion on current challenges in the field and future directions and finally by conclusion.
Genes & Development, 2007
The design of artificial biological systems and the understanding of their natural counterparts are key objectives of the emerging discipline of synthetic biology. Toward both ends, research in synthetic biology has primarily focused on the construction of simple devices, such as transcription-based oscillators and switches. Construction of such devices should provide us with insight on the design of natural systems, indicating whether our understanding is complete or whether there are still gaps in our knowledge. Construction of simple biological systems may also lay the groundwork for the construction of more complex systems that have practical utility. To realize its full potential, biological systems design borrows from the allied fields of protein design and metabolic engineering. In this review, we describe the scientific accomplishments in this field, as well as its forays into biological part standardization and education of future biological designers.
Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering.