Understanding and exploiting feedback in synthetic biology

Afroz, Taliman; Beisel, Chase L.

doi:10.1016/j.ces.2013.02.017

Cited by 28 publications

(20 citation statements)

References 94 publications

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“…Coupling positive and negative feedback has been shown to impart unique properties not ascribed to either mode of feedback alone (Thomas, 1978;Tian et al, 2009;Shah and Sarkar, 2011;Afroz and Beisel, 2013). For instance, natural and synthetic gene regulatory networks that feature positive and negative feedback have been reported to exhibit ranging behaviours (Brandman and Meyer, 2008), such as stable oscillations within synthetic transcriptional networks (Atkinson et al, 2003;Stricker et al, 2008;Tigges et al, 2009;Biliouris et al, 2012;Prindle et al, 2012), excitability within the uptake of foreign DNA (Süel et al, 2006), and bistability with limited memory within the transcriptional response to D-galactose in yeast (Acar et al, 2005;Avendaño et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Bacterial sugar utilization gives rise to distinct single‐cell behaviours

Afroz

Biliouris

Kaznessis

et al. 2014

Molecular Microbiology

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Inducible utilization pathways reflect widespread microbial strategies to uptake and consume sugars from the environment. Despite their broad importance and extensive characterization, little is known how these pathways naturally respond to their inducing sugar in individual cells. Here, we performed single-cell analyses to probe the behavior of representative pathways in the model bacterium Escherichia coli. We observed diverse single-cell behaviors, including uniform responses (D-lactose, D-galactose, N-acetylglucosamine, N-acetylneuraminic acid), “all-or-none” responses (D-xylose, L-rhamnose), and complex combinations thereof (L-arabinose, D-gluconate). Mathematical modeling and probing of genetically modified pathways revealed that the simple framework underlying these pathways—inducible transport and inducible catabolism—could give rise to most of these behaviors. Sugar catabolism was also an important feature, as disruption of catabolism eliminated tunable induction as well as enhanced memory of previous conditions. For instance, disruption of catabolism in pathways that respond to endogenously synthesized sugars led to full pathway induction even in the absence of exogenous sugar. Our findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering.

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Section: Introductionmentioning

confidence: 99%

Bacterial sugar utilization gives rise to distinct single‐cell behaviours

Afroz

Biliouris

Kaznessis

et al. 2014

Molecular Microbiology

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“…Despite the fact that a large volume of regulatory architectures and motifs has been discovered (2,3), little has been accomplished in pathway engineering to improve cellular productivity and yield by exploiting dynamic pathway regulation and metabolic control (4). One essential part in implementing synthetic metabolic control in pathway engineering is to engineer novel metabolite sensors with desired input-output relationships.…”

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confidence: 99%

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

Zhang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

434

356

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Global energy demand and environmental concerns have stimulated increasing efforts to produce carbon-neutral fuels directly from renewable resources. Microbially derived aliphatic hydrocarbons, the petroleum-replica fuels, have emerged as promising alternatives to meet this goal. However, engineering metabolic pathways with high productivity and yield requires dynamic redistribution of cellular resources and optimal control of pathway expression. Here we report a genetically encoded metabolic switch that enables dynamic regulation of fatty acids (FA) biosynthesis in Escherichia coli. The engineered strains were able to dynamically compensate the critical enzymes involved in the supply and consumption of malonyl-CoA and efficiently redirect carbon flux toward FA biosynthesis. Implementation of this metabolic control resulted in an oscillatory malonyl-CoA pattern and a balanced metabolism between cell growth and product formation, yielding 15.7-and 2.1-fold improvement in FA titer compared with the wild-type strain and the strain carrying the uncontrolled metabolic pathway. This study provides a new paradigm in metabolic engineering to control and optimize metabolic pathways facilitating the high-yield production of other malonyl-CoA-derived compounds.biofuels | dynamic metabolic control | transcriptional regulation A grand challenge in synthetic biology is to move the design of biomolecular circuits from purely genetic constructs toward systems that integrate different levels of cellular complexity, including regulatory networks and metabolic pathways (1). Despite the fact that a large volume of regulatory architectures and motifs has been discovered (2, 3), little has been accomplished in pathway engineering to improve cellular productivity and yield by exploiting dynamic pathway regulation and metabolic control (4). One essential part in implementing synthetic metabolic control in pathway engineering is to engineer novel metabolite sensors with desired input-output relationships. For example, have designed and applied a regulatory circuit that can sense the glycolytic pathway hallmark metabolite acetylphosphate to control the lycopene biosynthetic pathway (5) and generate oscillatory gene expression (6) as well as achieve artificial cell-cell communication (7). Dahl et al. (8) have used stressresponse promoters to improve farnesyl pyrophosphate production, and Tsao et al. (9) have rewired the Escherichia coli native quorumsensing regulon for autonomous induction of recombinant proteins.Traditional metabolic engineering is largely focused on the overexpression of rate-limiting steps (10

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“…Negative feedback is a widely observed regulatory mechanism in natural and artificial systems, and is found in different biological processes such as transcription, translation and protein signalling. This mechanism imbues the system with properties such as an ultrasensitive response or short rising time [18]. We explored whether, with a negative feedback, a gene with high dosage in the genome will show different expression profiles compared with single copy.…”

Section: High Dosages Of Self-inhibiting Gene Facilitate Monoallelic mentioning

confidence: 99%

High gene dosage changes transcriptional regulation of genetic structures and contributes to diversity and heterogeneity

Hannam

Albergante

2018

Preprint

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Differences in gene dosages between and within species are widely observed. Nevertheless, our understanding of the impacts of gene dosages on transcriptional regulation is far from complete and it is largely ignored in many genetic studies. In this article, we showed that dynamic properties of three genetic structures became significantly different when gene dosages were high and, for self-inhibiting genes, high gene dosages could facilitate monoallelic expression at single cell level and heterogeneity of cell population. This shed lights on potential links between levels of ploidy and phenotypes. In addition, in the context of modern molecular biology, especially synthetic biology, gene dosage needs to be taken into consideration when designing or modifying genetic circuits.

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Understanding and exploiting feedback in synthetic biology

Cited by 28 publications

References 94 publications

Bacterial sugar utilization gives rise to distinct single‐cell behaviours

Bacterial sugar utilization gives rise to distinct single‐cell behaviours

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

High gene dosage changes transcriptional regulation of genetic structures and contributes to diversity and heterogeneity

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