Literature DB >> 27440256

Control theory meets synthetic biology.

Domitilla Del Vecchio1, Aaron J Dy2, Yili Qian3.   

Abstract

The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology.
© 2016 The Author(s).

Keywords:  control theory; feedback; gene regulation; genetic circuits; robustness; synthetic biology

Mesh:

Year:  2016        PMID: 27440256      PMCID: PMC4971224          DOI: 10.1098/rsif.2016.0380

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN: 1742-5662            Impact factor:   4.118


  100 in total

1.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

2.  Engineering static and dynamic control of synthetic pathways.

Authors:  William J Holtz; Jay D Keasling
Journal:  Cell       Date:  2010-01-08       Impact factor: 41.582

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.  Programmable bacteria detect and record an environmental signal in the mammalian gut.

Authors:  Jonathan W Kotula; S Jordan Kerns; Lev A Shaket; Layla Siraj; James J Collins; Jeffrey C Way; Pamela A Silver
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-17       Impact factor: 11.205

Review 5.  DNA modification and restriction.

Authors:  W Arber; S Linn
Journal:  Annu Rev Biochem       Date:  1969       Impact factor: 23.643

Review 6.  Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance.

Authors:  Dietmar Werner Hutmacher; Boris Michael Holzapfel; Elena Maria De-Juan-Pardo; Brooke Anne Pereira; Stuart John Ellem; Daniela Loessner; Gail Petuna Risbridger
Journal:  Curr Opin Biotechnol       Date:  2015-06-26       Impact factor: 9.740

7.  A model for improving microbial biofuel production using a synthetic feedback loop.

Authors:  Mary J Dunlop; Jay D Keasling; Aindrila Mukhopadhyay
Journal:  Syst Synth Biol       Date:  2010-02-25

Review 8.  Engineering Stem Cell Organoids.

Authors:  Xiaolei Yin; Benjamin E Mead; Helia Safaee; Robert Langer; Jeffrey M Karp; Oren Levy
Journal:  Cell Stem Cell       Date:  2016-01-07       Impact factor: 24.633

9.  Substrate-dependent control of MAPK phosphorylation in vivo.

Authors:  Yoosik Kim; Ze'ev Paroush; Knud Nairz; Ernst Hafen; Gerardo Jiménez; Stanislav Y Shvartsman
Journal:  Mol Syst Biol       Date:  2011-02-01       Impact factor: 11.429

10.  Synthetic feedback control using an RNAi-based gene-regulatory device.

Authors:  Ryan J Bloom; Sally M Winkler; Christina D Smolke
Journal:  J Biol Eng       Date:  2015-04-14       Impact factor: 4.355

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  32 in total

1.  Synthetic negative feedback circuits using engineered small RNAs.

Authors:  Ciarán L Kelly; Andreas W K Harris; Harrison Steel; Edward J Hancock; John T Heap; Antonis Papachristodoulou
Journal:  Nucleic Acids Res       Date:  2018-10-12       Impact factor: 16.971

2.  Analysis of productivity and stability of synthetic microbial communities.

Authors:  Sihao Di; Aidong Yang
Journal:  J R Soc Interface       Date:  2019-01-31       Impact factor: 4.118

Review 3.  Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.

Authors:  Madalena Chaves; Hidde de Jong
Journal:  Methods Mol Biol       Date:  2021

Review 4.  Control and regulation of pathways via negative feedback.

Authors:  Herbert M Sauro
Journal:  J R Soc Interface       Date:  2017-02       Impact factor: 4.118

5.  Optimal control of bacterial growth for the maximization of metabolite production.

Authors:  Ivan Yegorov; Francis Mairet; Hidde de Jong; Jean-Luc Gouzé
Journal:  J Math Biol       Date:  2018-10-17       Impact factor: 2.259

6.  Realizing 'integral control' in living cells: how to overcome leaky integration due to dilution?

Authors:  Yili Qian; Domitilla Del Vecchio
Journal:  J R Soc Interface       Date:  2018-02       Impact factor: 4.118

7.  Optimization-based synthesis of stochastic biocircuits with statistical specifications.

Authors:  Yuta Sakurai; Yutaka Hori
Journal:  J R Soc Interface       Date:  2018-01       Impact factor: 4.118

8.  Dynamic metabolic control: towards precision engineering of metabolism.

Authors:  Di Liu; Ahmad A Mannan; Yichao Han; Diego A Oyarzún; Fuzhong Zhang
Journal:  J Ind Microbiol Biotechnol       Date:  2018-01-29       Impact factor: 3.346

9.  Cell-machine interfaces for characterizing gene regulatory network dynamics.

Authors:  Jean-Baptiste Lugagne; Mary J Dunlop
Journal:  Curr Opin Syst Biol       Date:  2019-02-01

10.  Signaling pathways as linear transmitters.

Authors:  Harry Nunns; Lea Goentoro
Journal:  Elife       Date:  2018-09-19       Impact factor: 8.140

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