1
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Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
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Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
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2
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Gupta D, Sharma G, Saraswat P, Ranjan R. Synthetic Biology in Plants, a Boon for Coming Decades. Mol Biotechnol 2021; 63:1138-1154. [PMID: 34420149 DOI: 10.1007/s12033-021-00386-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/16/2021] [Indexed: 02/01/2023]
Abstract
Recently an enormous expansion of knowledge is seen in various disciplines of science. This surge of information has given rise to concept of interdisciplinary fields, which has resulted in emergence of newer research domains, one of them is 'Synthetic Biology' (SynBio). It captures basics from core biology and integrates it with concepts from the other areas of study such as chemical, electrical, and computational sciences. The essence of synthetic biology is to rewire, re-program, and re-create natural biological pathways, which are carried through genetic circuits. A genetic circuit is a functional assembly of basic biological entities (DNA, RNA, proteins), created using typical design, built, and test cycles. These circuits allow scientists to engineer nearly all biological systems for various useful purposes. The development of sophisticated molecular tools, techniques, genomic programs, and ease of nucleic acid synthesis have further fueled several innovative application of synthetic biology in areas like molecular medicines, pharmaceuticals, biofuels, drug discovery, metabolomics, developing plant biosensors, utilization of prokaryotic systems for metabolite production, and CRISPR/Cas9 in the crop improvement. These applications have largely been dominated by utilization of prokaryotic systems. However, newer researches have indicated positive growth of SynBio for the eukaryotic systems as well. This paper explores advances of synthetic biology in the plant field by elaborating on its core components and potential applications. Here, we have given a comprehensive idea of designing, development, and utilization of synthetic biology in the improvement of the present research state of plant system.
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Affiliation(s)
- Dipinte Gupta
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Gauri Sharma
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Pooja Saraswat
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Rajiv Ranjan
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India.
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3
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Vernuccio S, Broadbelt LJ. Discerning complex reaction networks using automated generators. AIChE J 2019. [DOI: 10.1002/aic.16663] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sergio Vernuccio
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
| | - Linda J. Broadbelt
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
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4
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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5
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Abstract
With inexpensive DNA synthesis technologies, we can now construct biological systems by quickly piecing together DNA sequences. Synthetic biology is the promising discipline that focuses on the construction of these new biological systems. Synthetic biology is an engineering discipline, and as such, it can benefit from mathematical modeling. This chapter focuses on mathematical models of biological systems. These models take the form of chemical reaction networks. The importance of stochasticity is discussed and methods to simulate stochastic reaction networks are reviewed. A closure scheme solution is also presented for the master equation of chemical reaction networks. The master equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks for over 70 years. With the first complete solution of chemical master equations, a wide range of experimental observations of biomolecular interactions may be mathematically conceptualized. We anticipate that models based on the closure scheme described herein may assist in rationally designing synthetic biological systems.
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6
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Liu W, Stewart CN. Plant synthetic biology. TRENDS IN PLANT SCIENCE 2015; 20:309-317. [PMID: 25825364 DOI: 10.1016/j.tplants.2015.02.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 02/11/2015] [Accepted: 02/25/2015] [Indexed: 05/18/2023]
Abstract
Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants.
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Affiliation(s)
- Wusheng Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996-4561, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996-4561, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6037, USA.
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7
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Bolintineanu DS, Volzing K, Vivcharuk V, Sayyed-Ahmad A, Srivastava P, Kaznessis YN. Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2014; 59:3167-3176. [PMID: 25308994 PMCID: PMC4191592 DOI: 10.1021/je500225x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/01/2014] [Indexed: 05/17/2023]
Abstract
The tetracycline operon is an important gene network component, commonly used in synthetic biology applications because of its switch-like character. At the heart of this system is the highly specific interaction of the tet repressor protein (TetR) with its cognate DNA sequence (tetO). TetR binding on tetO practically stops expression of genes downstream of tetO by excluding RNA polymerase from binding the promoter and initiating transcription. Mutating the tetO sequence alters the strength of TetR-tetO binding and thus provides a tool to synthetic biologists to manipulate gene expression levels. We employ molecular dynamics (MD) simulations coupled with the free energy perturbation method to investigate the binding affinity of TetR to different tetO mutants. We also carry out in vivo tests in Escherichia coli for a series of promoters based on these mutants. We obtain reasonable agreement between experimental green fluorescent protein (GFP) repression levels and binding free energy differences computed from molecular simulations. In all cases, the wild-type tetO sequence yields the strongest TetR binding, which is observed both experimentally, in terms of GFP levels, and in simulation, in terms of free energy changes. Two of the four tetO mutants we tested yield relatively strong binding, whereas the other two mutants tend to be significantly weaker. The clustering and relative ranking of this subset of tetO mutants is generally consistent between our own experimental data, previous experiments with different systems and the free energy changes computed from our simulations. Overall, this work offers insights into an important synthetic biological system and demonstrates the potential, as well as limitations of molecular simulations to quantitatively explain biologically relevant behavior.
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Affiliation(s)
| | | | | | | | | | - Yiannis N. Kaznessis
- E-mail: . Phone: 612-624-4197 Fax: 612-626-7246. Address: 253 Amundson Hall 421 Washington Ave SE Minneapolis, MN
55455, United States
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8
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Smadbeck P, Kaznessis YN. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks. Curr Opin Chem Eng 2014; 5:90-95. [PMID: 25215268 DOI: 10.1016/j.coche.2014.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized.
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Affiliation(s)
- Patrick Smadbeck
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Zhuo Y, Zhang T, Wang Q, Cruz-Morales P, Zhang B, Liu M, Barona-Gómez F, Zhang L. Synthetic biology of avermectin for production improvement and structure diversification. Biotechnol J 2014; 9:316-25. [PMID: 24478271 DOI: 10.1002/biot.201200383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 10/26/2013] [Accepted: 12/24/2013] [Indexed: 01/15/2023]
Abstract
Natural products are still key sources of current clinical drugs and innovative therapeutic agents. Since wild-type microorganisms only produce natural products in very small quantities, yields of production strains need to be improved by breaking down the precise genetic and biochemical circuitry. Herein, we use avermectins as an example of production improvement and chemical structure diversification by synthetic biology. Avermectins are macrocyclic lactones produced by Streptomyces avermitilis and are well known and widely used for antiparasitic therapy. Given the importance of this molecule and its derivatives, many efforts and strategies were employed to improve avermectin production and generate new active analogues. This review describes the current status of synthetic strategies successfully applied for developing natural-product-producing strains and discusses future prospects for the application of enhanced avermectin production.
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Affiliation(s)
- Ying Zhuo
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
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10
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11
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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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12
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Cox RS, Nishikata K, Shimoyama S, Yoshida Y, Matsui M, Makita Y, Toyoda T. PromoterCAD: Data-driven design of plant regulatory DNA. Nucleic Acids Res 2013; 41:W569-74. [PMID: 23766287 PMCID: PMC3692106 DOI: 10.1093/nar/gkt518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Synthetic promoters can control the timing, location and amount of gene expression for any organism. PromoterCAD is a web application for designing synthetic promoters with altered transcriptional regulation. We use a data-first approach, using published high-throughput expression and motif data from for Arabidopsis thaliana to guide DNA design. We demonstrate data mining tools for finding motifs related to circadian oscillations and tissue-specific expression patterns. PromoterCAD is built on the LinkData open platform for data publication and rapid web application development, allowing new data to be easily added, and the source code modified to add new functionality. PromoterCAD URL: http://promotercad.org. LinkData URL: http://linkdata.org.
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Affiliation(s)
- Robert Sidney Cox
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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13
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Abstract
As the complexity of synthetic genetic circuits increases, modeling is becoming a necessary first step to inform subsequent experimental efforts. In recent years, the design automation community has developed a wealth of computational tools for assisting experimentalists in designing and analyzing new genetic circuits at several scales. However, existing software primarily caters to either the DNA- or single-cell level, with little support for the multicellular level. To address this need, the iBioSim software package has been enhanced to provide support for modeling, simulating, and visualizing dynamic cellular populations in a two-dimensional space. This capacity is fully integrated into the software, capitalizing on iBioSim's strengths in modeling, simulating, and analyzing single-celled systems.
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Affiliation(s)
- Jason T. Stevens
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Chris J. Myers
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United
States
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14
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15
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Volzing K, Biliouris K, Smadbeck P, Kaznessis Y. Computer-Aided Design of Synthetic Biological Constructs with the Synthetic Biology Software Suite. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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16
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Lee SY, Sohn SB, Kim YB, Shin JH, Kim JE, Kim TY. Computational Methods for Strain Design. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00008-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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17
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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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18
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Smadbeck P, Kaznessis Y. Stochastic model reduction using a modified Hill-type kinetic rate law. J Chem Phys 2012; 137:234109. [PMID: 23267473 DOI: 10.1063/1.4770273] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the present work, we address a major challenge facing the modeling of biochemical reaction networks: when using stochastic simulations, the computational load and number of unknown parameters may dramatically increase with system size and complexity. A proposed solution to this challenge is the reduction of models by utilizing nonlinear reaction rate laws in place of a complex multi-reaction mechanism. This type of model reduction in stochastic systems often fails when applied outside of the context in which it was initially conceived. We hypothesize that the use of nonlinear rate laws fails because a single reaction is inherently Poisson distributed and cannot match higher order statistics. In this study we explore the use of Hill-type rate laws as an approximation for gene regulation, specifically transcription repression. We matched output data for several simple gene networks to determine Hill-type parameters. We show that the models exhibit inaccuracies when placed into a simple feedback repression model. By adding an additional abstract reaction to the models we account for second-order statistics. This split Hill rate law matches higher order statistics and demonstrates that the new model is able to more accurately describe the mean protein output. Finally, the modified Hill model is shown to be modular and models retain accuracy when placed into a larger multi-gene network. The work as presented may be used in gene regulatory or cell-signaling networks, where multiple binding events can be captured by Hill kinetics. The added benefit of the proposed split-Hill kinetics is the improved accuracy in modeling stochastic effects. We demonstrate these benefits with a few specific reaction network examples.
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Affiliation(s)
- Patrick Smadbeck
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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19
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Quo CF, Kaddi C, Phan JH, Zollanvari A, Xu M, Wang MD, Alterovitz G. Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. Brief Bioinform 2012; 13:430-45. [PMID: 22833495 DOI: 10.1093/bib/bbs026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Recent advances in high-throughput biotechnologies have led to the rapid growing research interest in reverse engineering of biomolecular systems (REBMS). 'Data-driven' approaches, i.e. data mining, can be used to extract patterns from large volumes of biochemical data at molecular-level resolution while 'design-driven' approaches, i.e. systems modeling, can be used to simulate emergent system properties. Consequently, both data- and design-driven approaches applied to -omic data may lead to novel insights in reverse engineering biological systems that could not be expected before using low-throughput platforms. However, there exist several challenges in this fast growing field of reverse engineering biomolecular systems: (i) to integrate heterogeneous biochemical data for data mining, (ii) to combine top-down and bottom-up approaches for systems modeling and (iii) to validate system models experimentally. In addition to reviewing progress made by the community and opportunities encountered in addressing these challenges, we explore the emerging field of synthetic biology, which is an exciting approach to validate and analyze theoretical system models directly through experimental synthesis, i.e. analysis-by-synthesis. The ultimate goal is to address the present and future challenges in reverse engineering biomolecular systems (REBMS) using integrated workflow of data mining, systems modeling and synthetic biology.
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Affiliation(s)
- Chang F Quo
- Georgia Institute of Technology, Atlanta, GA 30332, USA
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20
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Synthetic genomics: potential and limitations. Curr Opin Biotechnol 2012; 23:659-65. [DOI: 10.1016/j.copbio.2012.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 01/23/2012] [Accepted: 01/24/2012] [Indexed: 11/22/2022]
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21
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García Adeva J, Reynolds M. Web-based simulation of fruit fly to support biosecurity decision-making. ECOL INFORM 2012. [DOI: 10.1016/j.ecoinf.2012.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Abstract
As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology.
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23
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Abstract
Computational synthetic biology has borrowed methods, concepts, and techniques from systems biology and electrical engineering. Features of tools for the analysis of biochemical networks and the design of electric circuits have been combined to develop new software, where Standard Biological Parts (physically stored at the MIT Registry) have a mathematical description, based on mass action or Hill kinetics, and can be assembled into genetic networks in a visual, "drag & drop" fashion. Recent tools provide the user with databases, simulation environments, formal languages, and even algorithms for circuit automatic design to refine and speed up gene network construction. Moreover, advances in automation of DNA assembly indicate that synthetic biology software soon will drive the wet-lab implementation of DNA sequences.
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24
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Volzing K, Biliouris K, Kaznessis YN. proTeOn and proTeOff, new protein devices that inducibly activate bacterial gene expression. ACS Chem Biol 2011; 6:1107-16. [PMID: 21819083 DOI: 10.1021/cb200168y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Using an original workflow, we have modeled, constructed, and characterized two new molecular devices that inducibly activate gene expression in Escherichia coli. The devices, prokaryotic-TetOn and prokaryotic-TetOff, were built by fusing an inducible DNA-binding protein domain to a transcription activation domain and constructing a complementary synthetic promoter sequence through which they could control downstream gene expression. In particular, the transactivators were built using variants of the tetracycline repressor, TetR, and the transactivating domain of the LuxR activator. The complementary promoter sequence included TetR's operator, tetO, and elements of the lux promoter. These specific protein domains and their operator sites were chosen as they have been thoroughly studied and well characterized. First, our methodology began with optimizing the geometry of the molecular components using molecular modeling. We did so to achieve an unprecedented combination of controllable and transactivating function in bacterial organisms. The devices were then built to activate the expression of green fluorescent protein. Their unique function was found to be robustly tight and activating many-fold increases of expressed gene levels, as measured by flow cytometry experiments. The devices were further characterized with stochastic kinetic models. The new devices presented herein may become useful additions to the molecular toolboxes used by biologists to control bacterial gene expression. The methodology used may also be a foundation for the design, development, and characterization of a library of such devices and more complex gene regulatory networks.
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Affiliation(s)
- Katherine Volzing
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Konstantinos Biliouris
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yiannis N. Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
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25
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Wilson ML, Hertzberg R, Adam L, Peccoud J. A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. Methods Enzymol 2011; 498:173-88. [PMID: 21601678 DOI: 10.1016/b978-0-12-385120-8.00008-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific to a domain, organization, or project. Design strategies include limited sets of user-defined parts and rules indicating how these parts are to be combined in genetic constructs. In addition to reducing design time to minutes, GenoCAD improves the quality and reliability of the finished sequence by ensuring that the designs follow established rules of sequence construction. GenoCAD.org is a publicly available instance of GenoCAD that can be found at www.genocad.org. The source code and latest build are available from SourceForge to allow advanced users to install and customize GenoCAD for their unique needs. This chapter focuses primarily on how the GenoCAD tools can be used to organize genetic parts into customized personal libraries, then how these libraries can be used to design sequences. In addition, GenoCAD's parts management system and search capabilities are described in detail. Instructions are provided for installing a local instance of GenoCAD on a server. Some of the future enhancements of this rapidly evolving suite of applications are briefly described.
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Affiliation(s)
- Mandy L Wilson
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
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SynBioSS-aided design of synthetic biological constructs. Methods Enzymol 2011. [PMID: 21601676 DOI: 10.1016/b978-0-12-385120-8.00006-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We present walkthrough examples of using SynBioSS to design, model, and simulate synthetic gene regulatory networks. SynBioSS stands for Synthetic Biology Software Suite, a platform that is publicly available with Open Licenses at www.synbioss.org. An important aim of computational synthetic biology is the development of a mathematical modeling formalism that is applicable to a wide variety of simple synthetic biological constructs. SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to known synthetic biological systems, such as bistable switches, AND gates, and oscillators. Here, we discuss how SynBioSS creates links between DNA sequences and targeted dynamic phenotypes of these simple systems.
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Abstract
Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. We illustrate the collection by building several model contructs, including concatemers of protein binding-site motifs, and a variety of plasmids for eukaryotic stable cloning and chromosomal insertion. For example, in 3 biobrick iterations, we make a cerulean-reporter plasmid for cloning fluorescent protein fusions. Furthermore, we use the collection to implement a recombinase-mediated DNA insertion (RMDI), allowing chromosomal site-directed exchange of genes. By making one recipient stable cell line, many standardised cell lines can subsequently be generated, by fluorescent fusion-gene exchange. We propose that this biobrick collection may be distributed peer-to-peer as a stand-alone library, in addition to its distribution through the Registry of Standard Biological Parts (http://partsregistry.org/).
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Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Anderson JC, Densmore D. Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 2011; 6:e18882. [PMID: 21559524 PMCID: PMC3084710 DOI: 10.1371/journal.pone.0018882] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 03/24/2011] [Indexed: 11/19/2022] Open
Abstract
Background Synthetic biological systems are currently created by an ad-hoc, iterative
process of specification, design, and assembly. These systems would greatly
benefit from a more formalized and rigorous specification of the desired
system components as well as constraints on their composition. Therefore,
the creation of robust and efficient design flows and tools is imperative.
We present a human readable language (Eugene) that allows for the
specification of synthetic biological designs based on biological parts, as
well as provides a very expressive constraint system to drive the automatic
creation of composite Parts (Devices) from a collection of individual
Parts. Results We illustrate Eugene's capabilities in three different areas: Device
specification, design space exploration, and assembly and simulation
integration. These results highlight Eugene's ability to create
combinatorial design spaces and prune these spaces for simulation or
physical assembly. Eugene creates functional designs quickly and
cost-effectively. Conclusions Eugene is intended for forward engineering of DNA-based devices, and through
its data types and execution semantics, reflects the desired abstraction
hierarchy in synthetic biology. Eugene provides a powerful constraint system
which can be used to drive the creation of new devices at runtime. It
accomplishes all of this while being part of a larger tool chain which
includes support for design, simulation, and physical device assembly.
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Affiliation(s)
- Lesia Bilitchenko
- Department of Computer Science, California
State Polytechnic University, Pomona, California, United States of
America
| | - Adam Liu
- Department of Electrical Engineering and
Computer Sciences, University of California, Berkeley, California, United States
of America
| | - Sherine Cheung
- Department of Bioengineering, University of
California San Diego, La Jolla, California, United States of America
| | - Emma Weeding
- Department of Chemical Engineering and
Materials Science, University of Minnesota, Minneapolis, Minnesota, United
States of America
| | - Bing Xia
- Department of Electrical Engineering and
Computer Sciences, University of California, Berkeley, California, United States
of America
| | - Mariana Leguia
- Department of Bioengineering, QB3: California
Institute for Quantitative Biological Research, University of California,
Berkeley, California, United States of America
| | - J. Christopher Anderson
- Department of Bioengineering, QB3: California
Institute for Quantitative Biological Research, University of California,
Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence
Berkeley National Laboratory, Berkeley, California, United States of
America
| | - Douglas Densmore
- Department of Electrical and Computer
Engineering, Boston University, Boston, Massachusetts, United States of
America
- * E-mail:
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Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Standard biological parts knowledgebase. PLoS One 2011; 6:e17005. [PMID: 21390321 PMCID: PMC3044748 DOI: 10.1371/journal.pone.0017005] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 01/19/2011] [Indexed: 11/19/2022] Open
Abstract
We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.
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Affiliation(s)
- Michal Galdzicki
- Biomedical & Health Informatics, University of Washington, Seattle, Washington, United States of America
| | - Cesar Rodriguez
- BIOFAB, University of California, Berkeley, California, United States of America
| | - Deepak Chandran
- Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Herbert M. Sauro
- Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - John H. Gennari
- Biomedical & Health Informatics, University of Washington, Seattle, Washington, United States of America
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Kaznessis YN. Mathematical models in biology: from molecules to life. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 3:314-22. [PMID: 21472998 DOI: 10.1002/wsbm.142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A vexing question in the biological sciences is the following: can biological phenotypes be explained with mathematical models of molecules that interact according to physical laws? At the crux of the matter lies the doubt that humans can develop physically faithful mathematical representations of living organisms. We discuss advantages that synthetic biological systems confer that may help us describe life's distinctiveness with tractable mathematics that are grounded on universal laws of thermodynamics and molecular biology.
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Affiliation(s)
- Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, USA.
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Biliouris K, Daoutidis P, Kaznessis YN. Stochastic simulations of the tetracycline operon. BMC SYSTEMS BIOLOGY 2011; 5:9. [PMID: 21247421 PMCID: PMC3037858 DOI: 10.1186/1752-0509-5-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 01/19/2011] [Indexed: 11/30/2022]
Abstract
Background The tetracycline operon is a self-regulated system. It is found naturally in bacteria where it confers resistance to antibiotic tetracycline. Because of the performance of the molecular elements of the tetracycline operon, these elements are widely used as parts of synthetic gene networks where the protein production can be efficiently turned on and off in response to the presence or the absence of tetracycline. In this paper, we investigate the dynamics of the tetracycline operon. To this end, we develop a mathematical model guided by experimental findings. Our model consists of biochemical reactions that capture the biomolecular interactions of this intriguing system. Having in mind that small biological systems are subjects to stochasticity, we use a stochastic algorithm to simulate the tetracycline operon behavior. A sensitivity analysis of two critical parameters embodied this system is also performed providing a useful understanding of the function of this system. Results Simulations generate a timeline of biomolecular events that confer resistance to bacteria against tetracycline. We monitor the amounts of intracellular TetR2 and TetA proteins, the two important regulatory and resistance molecules, as a function of intrecellular tetracycline. We find that lack of one of the promoters of the tetracycline operon has no influence on the total behavior of this system inferring that this promoter is not essential for Escherichia coli. Sensitivity analysis with respect to the binding strength of tetracycline to repressor and of repressor to operators suggests that these two parameters play a predominant role in the behavior of the system. The results of the simulations agree well with experimental observations such as tight repression, fast gene expression, induction with tetracycline, and small intracellular TetR2 amounts. Conclusions Computer simulations of the tetracycline operon afford augmented insight into the interplay between its molecular components. They provide useful explanations of how the components and their interactions have evolved to best serve bacteria carrying this operon. Therefore, simulations may assist in designing novel gene network architectures consisting of tetracycline operon components.
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Affiliation(s)
- Konstantinos Biliouris
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, MN 55455, USA
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MacDonald JT, Barnes C, Kitney RI, Freemont PS, Stan GBV. Computational design approaches and tools for synthetic biology. Integr Biol (Camb) 2011; 3:97-108. [DOI: 10.1039/c0ib00077a] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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