Literature DB >> 29380150

Dynamic metabolic control: towards precision engineering of metabolism.

Di Liu1, Ahmad A Mannan2, Yichao Han1, Diego A Oyarzún3, Fuzhong Zhang4.   

Abstract

Advances in metabolic engineering have led to the synthesis of a wide variety of valuable chemicals in microorganisms. The key to commercializing these processes is the improvement of titer, productivity, yield, and robustness. Traditional approaches to enhancing production use the "push-pull-block" strategy that modulates enzyme expression under static control. However, strains are often optimized for specific laboratory set-up and are sensitive to environmental fluctuations. Exposure to sub-optimal growth conditions during large-scale fermentation often reduces their production capacity. Moreover, static control of engineered pathways may imbalance cofactors or cause the accumulation of toxic intermediates, which imposes burden on the host and results in decreased production. To overcome these problems, the last decade has witnessed the emergence of a new technology that uses synthetic regulation to control heterologous pathways dynamically, in ways akin to regulatory networks found in nature. Here, we review natural metabolic control strategies and recent developments in how they inspire the engineering of dynamically regulated pathways. We further discuss the challenges of designing and engineering dynamic control and highlight how model-based design can provide a powerful formalism to engineer dynamic control circuits, which together with the tools of synthetic biology, can work to enhance microbial production.

Keywords:  Biosensors; Dynamic metabolic control; Genetic circuits; Model-based design; Synthetic biology

Mesh:

Substances:

Year:  2018        PMID: 29380150     DOI: 10.1007/s10295-018-2013-9

Source DB:  PubMed          Journal:  J Ind Microbiol Biotechnol        ISSN: 1367-5435            Impact factor:   3.346


  76 in total

1.  Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production.

Authors:  Yuki Soma; Taizo Hanai
Journal:  Metab Eng       Date:  2015-04-20       Impact factor: 9.783

Review 2.  Posttranslational regulation of microbial metabolism.

Authors:  Karl Kochanowski; Uwe Sauer; Elad Noor
Journal:  Curr Opin Microbiol       Date:  2015-06-03       Impact factor: 7.934

3.  Decoupling Resource-Coupled Gene Expression in Living Cells.

Authors:  Tatenda Shopera; Lian He; Tolutola Oyetunde; Yinjie J Tang; Tae Seok Moon
Journal:  ACS Synth Biol       Date:  2017-05-04       Impact factor: 5.110

4.  Stochasticity of metabolism and growth at the single-cell level.

Authors:  Daniel J Kiviet; Philippe Nghe; Noreen Walker; Sarah Boulineau; Vanda Sunderlikova; Sander J Tans
Journal:  Nature       Date:  2014-09-03       Impact factor: 49.962

Review 5.  Development of biosensors and their application in metabolic engineering.

Authors:  Jie Zhang; Michael K Jensen; Jay D Keasling
Journal:  Curr Opin Chem Biol       Date:  2015-06-05       Impact factor: 8.822

6.  Metabolic Feedback Circuits Provide Rapid Control of Metabolite Dynamics.

Authors:  Di Liu; Fuzhong Zhang
Journal:  ACS Synth Biol       Date:  2018-01-08       Impact factor: 5.110

7.  Design and Construction of Generalizable RNA-Protein Hybrid Controllers by Level-Matched Genetic Signal Amplification.

Authors:  Yen-Hsiang Wang; Maureen McKeague; Tammy M Hsu; Christina D Smolke
Journal:  Cell Syst       Date:  2016-11-10       Impact factor: 10.304

8.  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 9.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

10.  Engineering an allosteric transcription factor to respond to new ligands.

Authors:  Noah D Taylor; Alexander S Garruss; Rocco Moretti; Sum Chan; Mark A Arbing; Duilio Cascio; Jameson K Rogers; Farren J Isaacs; Sriram Kosuri; David Baker; Stanley Fields; George M Church; Srivatsan Raman
Journal:  Nat Methods       Date:  2015-12-21       Impact factor: 28.547

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  24 in total

Review 1.  Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.

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

2.  Prediction of Cellular Burden with Host-Circuit Models.

Authors:  Evangelos-Marios Nikolados; Andrea Y Weiße; Diego A Oyarzún
Journal:  Methods Mol Biol       Date:  2021

3.  Changing Form and Function through Carotenoids and Synthetic Biology.

Authors:  Eleanore T Wurtzel
Journal:  Plant Physiol       Date:  2018-10-25       Impact factor: 8.340

Review 4.  Incorporation of nonstandard amino acids into proteins: principles and applications.

Authors:  Tianwen Wang; Chen Liang; Hongjv Xu; Yafei An; Sha Xiao; Mengyuan Zheng; Lu Liu; Lei Nie
Journal:  World J Microbiol Biotechnol       Date:  2020-04-08       Impact factor: 3.312

Review 5.  Recent advances in improving metabolic robustness of microbial cell factories.

Authors:  Tian Jiang; Chenyi Li; Yuxi Teng; Ruihua Zhang; Yajun Yan
Journal:  Curr Opin Biotechnol       Date:  2020-07-16       Impact factor: 9.740

Review 6.  Prospects for engineering dynamic CRISPR-Cas transcriptional circuits to improve bioproduction.

Authors:  Jason Fontana; William E Voje; Jesse G Zalatan; James M Carothers
Journal:  J Ind Microbiol Biotechnol       Date:  2018-05-08       Impact factor: 3.346

7.  Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria.

Authors:  Chenyi Li; Yusong Zou; Tian Jiang; Jianli Zhang; Yajun Yan
Journal:  Metab Eng       Date:  2022-01-13       Impact factor: 9.783

8.  Stabilization of antithetic control via molecular buffering.

Authors:  Edward J Hancock; Diego A Oyarzún
Journal:  J R Soc Interface       Date:  2022-03-09       Impact factor: 4.118

Review 9.  Fine-tuning gene expression for improved biosynthesis of natural products: From transcriptional to post-translational regulation.

Authors:  Chenyi Li; Tian Jiang; Michelle Li; Yusong Zou; Yajun Yan
Journal:  Biotechnol Adv       Date:  2021-10-09       Impact factor: 14.227

10.  Designing an irreversible metabolic switch for scalable induction of microbial chemical production.

Authors:  Ahmad A Mannan; Declan G Bates
Journal:  Nat Commun       Date:  2021-06-08       Impact factor: 14.919

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