synthetic biology tools and applications pdf

Synthetic Biology Tools And Applications Pdf

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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.

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

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 integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research. The central dogma of biology is simply and elegantly stated; however it is less straightforward to engineer, control, and rewire for biotechnological purposes.

This difficulty stems from our limited understanding of the multiscale, and often stochastic, operation, and regulation of biological systems [ 1 — 3 ]. Nevertheless, rapid progress in uncovering the basic framework and information flow within the central dogma has helped fuel the current biotechnological revolution.

Yet, elucidating the specific components and control mechanisms inherent in this process has lagged significantly [ 4 — 6 ].

This limitation prevents the creation of custom-built cellular factories using modeling and de novo design. However, this limitation is only temporary. Recent advances in high-throughput biology are quickly uncovering the identity and details of these components and control schemes [ 7 — 10 ]. While not yet complete, this global, systems biology approach repeatedly depicts the central dogma as a multistep process subject to exquisite regulatory mechanisms established to maintain cellular homeostasis and to respond to environmental stimuli.

Once our understanding is advanced, it will be possible to synthetically create desired functions at all levels of the central dogma. The integrative complexity of the central dogma and biological systems in general has analogies and parallels to chemical or electrical systems. The rationale for drawing these analogies is twofold: 1 it helps to contextualize the various parts of a cellular process and 2 it facilitates the possible transfer of knowledge between the analogous systems.

In this regard, understanding the central dogma processes, the process controls, and the environmental influences within a cell is as vital as understanding analogous components within a traditional chemical factory. Uncovering and studying these components will ultimately lead to a factory-like cellular blueprint—a detailed catalogue of parts, interactions, and functions.

Moreover, compiling such a blueprint for all species will expand the number of parts we are able to access, characterize, and employ when trying to design cells and circuits from scratch. Thus, this understanding will enhance our ability to predict, control, and design cellular systems—major tenets in the emerging field of synthetic biology. Due to its youth, the field of synthetic biology has yet to have a concrete, comprehensive definition.

Yet, in its broadest sense, synthetic biology aims to harness the emergent properties of the central dogma for biotechnological and human use. This description of the field is comprehensive since even synthetically designed biological circuits actually interface with existing central dogma machinery in the cell.

In this regard, tools for synthetic biology harness the complexity of the central dogma process in a predictable, designed fashion. Within the context of engineering the central dogma, the seemingly wide variety of themes and aims in the synthetic biology research field become more unified. Considering the central dogma as a simple process diagram Figure 1 , it can be seen that the varied areas of synthetic biology research all influence the central dogma albeit at different access points in the process.

As Figure 1 illustrates, this system has three tiers, specifically: 1 the central dogma process units transcription and translation and associated streams DNA, RNA, and protein , 2 the intrinsic regulatory mechanisms in the cells, and 3 the extrinsic physical and chemical environment of the cells. These three tiers are depicted separately, but in reality are thoroughly enmeshed with one another as a result of evolved biological complexity.

Yet, this very complexity provides a multitude of access points, or nodes, for synthetic biologists to engineer. Synthetic biology research is at the forefront of engineering the three tiers of biological systems.

Contributions from systems biology have broadened our ability to understand and engineer biological networks [ 14 — 18 ], providing impetus for modifying tier two intrinsic control systems and tier three extrinsic signaling interactions. Other frontiers in synthetic biology have greatly expanded our capacity to construct and improve pathways and global cellular phenotype [ 19 — 24 ], which engineers the third tier interaction between proteins and the chemical environment.

In the same vein, protein engineering provides the synthetic biologist a great deal of flexibility for introducing and optimizing new function at any node [ 25 — 31 ], since proteins are such universal components throughout the central dogma process. All of these areas of synthetic biology are building toward a single goal: integrative control of the central dogma for biotechnological and human use. From this viewpoint, developing powerful new tools that manipulate biology at each of the three tiers will empower scientists and engineers with the ability to rewire and program cellular systems for both medical and biotechnological applications.

Combining these tools to work in concert would define the field of integrative synthetic biology. This culminating point of synthetic biology development will usher in the age of ground-up cellular design and optimization. However, much of current synthetic biology research is focused on tool development, a required foundation for integrative synthetic biology. As a result, it is not yet clear how to best integrate these approaches.

Therefore, the purpose of this review is to provide an overview of synthetic biology research, focusing on microbial hosts, and to highlight areas where more work must be done before realizing the potential of ground-up synthetic cellular engineering.

The first tier of synthetic biology focuses on altering the general process flow — specifically modifications to the function and behavior of the process units transcription [ 32 ] and translation and the associated process streams DNA, RNA [ 33 ], and protein. These manipulations are made possible through detailed knowledge of the central dogma process.

While this capacity has existed for several decades [ 34 ], novel capabilities and genetic tools afforded by synthetic biology may help overcome some of the limitations and time-consuming bottlenecks inherent in established techniques.

In this regard, synthetic biology aims to develop foundational technologies such as large-scale, economical de novo DNA synthesis [ 35 ] that would increase the efficiency of traditional recombinant DNA technology and genetic engineering. Collectively, synthetic engineering of the central dogma aims to optimize and expand the capabilities of native cellular machinery.

The methods and technologies developed from this research will contribute to a more powerful and efficient toolbox for the microbial engineer. In this section, we will review synthetic biology technologies and applications for influencing components within the first tier.

DNA manipulation began very early in the biotechnological revolution with recombinant DNA methods [ 36 — 38 ] and DNA sequencing technology [ 39 — 41 ]. Mutagenesis techniques and the establishment of standardized molecular biology methods [ 34 ] expanded these tools and empowered metabolic engineers with more powerful approaches to improve metabolic phenotypes [ 42 — 46 ]. Despite being straightforward and robust, these approaches are inherently limited by template-based DNA synthesis and restriction enzyme cloning.

However, inexpensive, large scale synthetic de novo DNA manufacturing technology has the potential to revolutionize this process once again. Unlike traditional methods, de novo synthesis removes the need to engineer cellular systems using preexisting DNA as a template.

In this regard, this technology brings about a new power to synthetically design genes, control elements, and circuits that do not exist in nature—thus creating novel function from the basic building blocks of nucleic acids and amino acids.

Moreover, improvements and new technologies are continually being published [ 12 , 35 , 47 — 50 ] which expand the potential applications and drive down prices. As a result, synthesis capabilities have moved beyond the scale of single genes and into the scale of chemically synthesized genomes [ 11 , 13 ].

Moreover, efforts are being made to introduce this synthetic DNA into a generic host [ 51 ] in an effort to completely reprogram a cell. The combination of these powerful new DNA synthesis techniques coupled with low-cost DNA sequencing has the potential to confer a great deal of freedom to researchers. With these advances, DNA design and cloning is no longer limited by existing fragments of template DNA and available restriction sites in plasmids. In essence, this technology serves as the basis for other synthetic biology tools, since DNA is the vehicle of almost every biological perturbation, regardless of the tier of interest.

However, our ability to create DNA de novo is not equally matched by a capacity to predict the ideal DNA sequence a priori for a given application. Attempts have been made to catalogue DNA elements [ 52 , 53 ] and predict the function of synthetic networks using models [ 9 , 15 , 17 , 18 , 54 ]. Nevertheless, our knowledge base for constructing predictive models of global cellular behavior is limited as is our ability to design large operons and circuits de novo.

Future work on characterizing these elements as well as their dynamics and interaction will allow for synthetically created custom-designed genetic circuits. Simply synthesizing and importing designed DNA is not enough to ensure desired function. Specifically, for these elements to operate efficiently, synthetic DNA operons must act independently and not be negatively influenced by other cellular processes.

One solution to mitigate this problem embodies another area of synthetic DNA engineering research: the quest for a minimal cell [ 55 — 57 ]. A minimal cell only contains the essential genetic information required to maintain viability under controlled conditions. In following with the industrial process analogy, this would correspond to a factory containing only the equipment necessary for a given process application. It is clear that this minimization makes sense in a process plant as superfluous equipment would be a waste of precious resources such as money and space.

However, cells contain many more parts than are necessary for a given biotechnological application. Recent advances in cataloging essential genes continue to move the minimal cell closer to reality [ 58 , 59 ]. However, it is currently unclear whether the genetic definition of a minimal cell will be generic or process specific. Thus, there may be a suite of minimal cells required; each one suited for different classes of bioproducts.

Another area of synthetic DNA engineering aims to expand the basic genetic code by adding synthetic base pairs [ 60 — 63 ]. Incorporating synthetic codons provides a means of utilizing nonnatural amino acids see Section 2. Already, alternative genetic codes have led to new applications for engineered biology [ 61 ].

One of the potential difficulties of incorporating synthetic base pairs into DNA is that the three-dimensional structure of the molecule may change and key binding proteins and polymerases may not be able to recognize the new genetic language.

However, initial results are promising [ 63 , 64 ] and suggest that drastic changes to innate cellular architecture are not required. Thus, alternative base pairs provide a newfound flexibility in genetic code and DNA manipulation technology. Furthermore, this approach is an excellent application for de novo DNA synthesis: the coupling of synthetic base pairs with DNA synthesis technology could create a powerful tool for designing synthetic circuits.

Regardless of the application, the capacity to engineer DNA using synthetic biology tools provides new access points to the cell unachievable by previous technology. Since the central dogma is so highly integrated, DNA-level perturbations can cause significant alterations in downstream process units Figure 1. As a result, microbial engineers must be able to synthetically optimize each of the process units.

The first process unit in the central dogma is transcription. A large number of proteins, small molecules, and even small RNAs can participate in this process step [ 5 ]. As a result, synthetic control of this process step influences the rate and capacity of mRNA synthesis. Not surprisingly, the key step of RNA polymerase II binding to a promoter sequence has been targeted by synthetic tools, such as promoter engineering, for the purposes of controlling gene expression levels [ 65 — 68 ].

By creating a library of promoter sequence mutants, a graduated expression profile can be developed. This resulting range of expression affords a more detailed investigation of expression levels beyond traditional wild type—knockout—strong overexpression studies.

Furthermore, well-characterized promoters enable more precise gene delivery [ 52 ]. A similar requirement for controlled expression is critical for genetic circuits where protein expression must be balanced to maintain a desired steady state. Often these circuits use inducible promoters, and a similar approach can be used to augment the expression capacity of inducible promoters.

Thus, well-documented genetic elements will be extremely useful in creating synthetic cells and circuits. However, transcription is a two-body problem requiring both proteins and DNA. Most previous work focused on the DNA aspect of the problem; however, proteins involved in transcription can also be engineered to synthetically control a cell [ 32 ].

Moreover, altering the DNA sequence focuses the change to one particular genetic locus, whereas changing the involved proteins has a profound, global impact.

It is often necessary to alter the transcriptional profile of many genes simultaneously to obtain a desired complex phenotype.

Synthetic Biology

It seems that you're in Germany. We have a dedicated site for Germany. The book uses an integrated approach to predict the behavior of various biological interactions. It further discusses how synthetic biology gathers the information about various systems, in order to either devise an entirely new system, or, to modulate existing systems. The book also tackles the concept of modularity, where biological systems are visualized in terms of their parts.

Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems. Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems.


PDF | Advances in synthetic biology have enabled the engineering of cells with genetic circuits in order to program cells with new biological.


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Synthetic biology aims to redesign and reconstruct living systems for understanding life or for useful real-world applications. In the past two decades, scientists have been able to use engineered living systems to produce many kinds of products from bioplastics to drugs, to construct a minimal bacterium with a fully synthetic genome and to store huge amount of information within a cell. And in , when the COVID pandemic swept across the world, the synthetic biology community became one of the major forces to develop effective diagnostic approaches as well as the drugs and vaccines, to rapidly cope with this great challenge with the state-of-the-art technologies in their hands. In this panel discussion held on 3rd August , eleven pioneering synthetic biologists from six countries across four continents gathered to discuss the development trend, challenges and biosafety issues concerning synthetic biology. Liu: Today we have a very distinguished panel from many countries around the world to discuss synthetic biology.

Synthetic biology SynBio is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. It is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biotechnology , genetic engineering , molecular biology , molecular engineering , systems biology , membrane science , biophysics , chemical and biological engineering , electrical and computer engineering , control engineering and evolutionary biology. Due to more powerful genetic engineering capabilities and decreased DNA synthesis and sequencing costs , the field of synthetic biology is rapidly growing. Synthetic biology has traditionally been divided into two different approaches: top down and bottom up.

NCBI Bookshelf. Biodefense in the Age of Synthetic Biology. This appendix describes a core set of current synthetic biology concepts, approaches, and tools that enable each step of the Design-Build-Test DBT cycle, focusing particularly on areas in which advances in biotechnology may raise the potential for malicious acts that were less feasible before the age of synthetic biology.

1 INTRODUCTION

NCBI Bookshelf. Biodefense in the Age of Synthetic Biology. To frame and guide the study, the relationship of synthetic biology to other areas of biotechnology was explored along with the context in which synthetic biology tools and applications are being pursued. Biotechnology is a broad term encompassing the application of biological components or processes to advance human purposes. Although the term itself is thought to have been in use for only about a century, humans have used various forms of biotechnology for millennia.

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.

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