Literature DB >> 28355534

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Bryan A Bartley1, Kyung Kim1, J Kyle Medley1, Herbert M Sauro2.   

Abstract

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties.
Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2017        PMID: 28355534      PMCID: PMC5376109          DOI: 10.1016/j.bpj.2017.02.013

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  69 in total

1.  Evolvability.

Authors:  Paul D Sniegowski; Helen A Murphy
Journal:  Curr Biol       Date:  2006-10-10       Impact factor: 10.834

Review 2.  A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future.

Authors:  James Chappell; Kyle E Watters; Melissa K Takahashi; Julius B Lucks
Journal:  Curr Opin Chem Biol       Date:  2015-06-18       Impact factor: 8.822

3.  Quantifying cellular capacity identifies gene expression designs with reduced burden.

Authors:  Francesca Ceroni; Rhys Algar; Guy-Bart Stan; Tom Ellis
Journal:  Nat Methods       Date:  2015-04-06       Impact factor: 28.547

4.  A whole-cell computational model predicts phenotype from genotype.

Authors:  Jonathan R Karr; Jayodita C Sanghvi; Derek N Macklin; Miriam V Gutschow; Jared M Jacobs; Benjamin Bolival; Nacyra Assad-Garcia; John I Glass; Markus W Covert
Journal:  Cell       Date:  2012-07-20       Impact factor: 41.582

5.  Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.

Authors:  Karsten Temme; Dehua Zhao; Christopher A Voigt
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-16       Impact factor: 11.205

6.  Evolvability and hierarchy in rewired bacterial gene networks.

Authors:  Mark Isalan; Caroline Lemerle; Konstantinos Michalodimitrakis; Carsten Horn; Pedro Beltrao; Emanuele Raineri; Mireia Garriga-Canut; Luis Serrano
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

7.  Programming cells by multiplex genome engineering and accelerated evolution.

Authors:  Harris H Wang; Farren J Isaacs; Peter A Carr; Zachary Z Sun; George Xu; Craig R Forest; George M Church
Journal:  Nature       Date:  2009-07-26       Impact factor: 49.962

8.  Rapid diversification of cell signaling phenotypes by modular domain recombination.

Authors:  Sergio G Peisajovich; Joan E Garbarino; Ping Wei; Wendell A Lim
Journal:  Science       Date:  2010-04-16       Impact factor: 47.728

9.  Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Authors:  Sheng Hui; Josh M Silverman; Stephen S Chen; David W Erickson; Markus Basan; Jilong Wang; Terence Hwa; James R Williamson
Journal:  Mol Syst Biol       Date:  2015-02-12       Impact factor: 11.429

10.  Stress-response balance drives the evolution of a network module and its host genome.

Authors:  Caleb González; Joe Christian J Ray; Michael Manhart; Rhys M Adams; Dmitry Nevozhay; Alexandre V Morozov; Gábor Balázsi
Journal:  Mol Syst Biol       Date:  2015-08-31       Impact factor: 11.429

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  7 in total

Review 1.  Mathematical Modelling in Plant Synthetic Biology.

Authors:  Anna Deneer; Christian Fleck
Journal:  Methods Mol Biol       Date:  2022

2.  Natural Environmental Variation Determines Microbial Diversity Patterns in Serofluid Dish, a Traditional Chinese Fermented Vegetable Food.

Authors:  Zhongkun Zhou; Rentao Zhang; Yunhao Ma; Kangjia Du; Mengze Sun; Hao Zhang; Xinrong Jiang; Hongyuan Tu; Peng Chen
Journal:  Curr Microbiol       Date:  2022-07-26       Impact factor: 2.343

3.  System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks.

Authors:  Julio A Freyre-González; Juan M Escorcia-Rodríguez; Luis F Gutiérrez-Mondragón; Jerónimo Martí-Vértiz; Camila N Torres-Franco; Andrea Zorro-Aranda
Journal:  Front Bioeng Biotechnol       Date:  2022-05-12

4.  BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts.

Authors:  Beibei Wang; Huayi Yang; Jianan Sun; Chuhao Dou; Jian Huang; Feng-Biao Guo
Journal:  Front Microbiol       Date:  2021-01-21       Impact factor: 5.640

5.  Modular Assembly of Ordered Hydrophilic Proteins Improve Salinity Tolerance in Escherichia coli.

Authors:  Leizhou Guo; Mingming Zhao; Yin Tang; Jiahui Han; Yuan Gui; Jiaming Ge; Shijie Jiang; Qilin Dai; Wei Zhang; Min Lin; Zhengfu Zhou; Jin Wang
Journal:  Int J Mol Sci       Date:  2021-04-25       Impact factor: 5.923

6.  An Efficient Modular Gateway Recombinase-Based Gene Stacking System for Generating Multi-Trait Transgenic Plants.

Authors:  Guannan Qin; Suting Wu; Liying Zhang; Yanyao Li; Chunmei Liu; Jianghui Yu; Lihua Deng; Guoying Xiao; Zhiguo Zhang
Journal:  Plants (Basel)       Date:  2022-02-11

Review 7.  Towards an engineering theory of evolution.

Authors:  Simeon D Castle; Claire S Grierson; Thomas E Gorochowski
Journal:  Nat Commun       Date:  2021-06-07       Impact factor: 14.919

  7 in total

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