Synthetic gene circuits for metabolic control: design trade-offs and constraints

Oyarzún, Diego A.; Stan, Guy-Bart

doi:10.1098/rsif.2012.0671

Cited by 73 publications

(69 citation statements)

References 48 publications

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“…Second, we have illustrated how to predict trade-offs between the induction level of a synthetic circuit, its function, and the growth of the host. We can therefore benchmark different designs aimed at producing chemicals in biotechnology, where circuits must operate robustly in different growth conditions (53,54). Third, disregulated biogenesis of ribosomes has been suggested as a driver for cancer development (55), and our model may help select, for example, therapeutic targets in the translation machinery.…”

Section: Applicationsmentioning

confidence: 99%

Mechanistic links between cellular trade-offs, gene expression, and growth

Weiße

Oyarzún

Danos

et al. 2015

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

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Intracellular processes rarely work in isolation but continually interact with the rest of the cell. In microbes, for example, we now know that gene expression across the whole genome typically changes with growth rate. The mechanisms driving such global regulation, however, are not well understood. Here we consider three trade-offs that, because of limitations in levels of cellular energy, free ribosomes, and proteins, are faced by all living cells and we construct a mechanistic model that comprises these trade-offs. Our model couples gene expression with growth rate and growth rate with a growing population of cells. We show that the model recovers Monod's law for the growth of microbes and two other empirical relationships connecting growth rate to the mass fraction of ribosomes. Further, we can explain growth-related effects in dosage compensation by paralogs and predict host-circuit interactions in synthetic biology. Simulating competitions between strains, we find that the regulation of metabolic pathways may have evolved not to match expression of enzymes to levels of extracellular substrates in changing environments but rather to balance a trade-off between exploiting one type of nutrient over another. Although coarse-grained, the trade-offs that the model embodies are fundamental, and, as such, our modeling framework has potentially wide application, including in both biotechnology and medicine.systems biology | synthetic biology | mathematical cell model | host-circuit interactions | evolutionarily stable strategy I ntracellular processes rarely work in isolation but continually interact with the rest of the cell. Yet often we study cellular processes with the implicit assumption that the remainder of the cell can either be ignored or provides a constant, background environment. Work in both systems and synthetic biology is, however, showing that this assumption is weak, at best. In microbes, growth rate can affect the expression both of single genes (1, 2) and across the entire genome (3-6). Specific control by transcription factors seems to be complemented by global, unspecific regulation that reflects the physiological state of the cell (5-7). Correspondingly, progress in synthetic biology is limited by two-way interactions between synthetic circuits and the host cell that cannot be designed away (8, 9).These phenomena are thought to arise from trade-offs where commitment of a finite intracellular resource to one response necessarily reduces the commitment of that resource to another response. A trade-off in the allocation of ribosomes has been suggested to underlie global gene regulation (2, 5). Similarly, depletion of finite resources and competition for cellular processes is thought to explain the failure of some synthetic circuits (8). Such circuits "load" the host cell, which can induce physiological responses that further degrade the function of the circuit (10). Our understanding of such trade-offs, however, is mostly phenomenological.Here we take an alternative approach and ask what new insi...

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Section: Applicationsmentioning

confidence: 99%

Mechanistic links between cellular trade-offs, gene expression, and growth

Weiße

Oyarzún

Danos

et al. 2015

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

Self Cite

375

500

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“…This type of regulation has been widely used in the field of dynamic metabolic engineering to promote and/ or 'robustify' biofuel production under changing environments [72 -75]. In [76], Oyarzú n & Stan provided detailed guidance on the selection of promoters and ribosome binding sites that reflects the trade-offs and constraints of transcriptional feedback for metabolic pathways. More broadly, feedback control has been extensively used in metabolic engineering, which is not the focus of this paper and an indepth review can be found elsewhere [77].…”

Section: Negative Feedback Implementationsmentioning

confidence: 99%

Control theory meets synthetic biology

Vecchio

Qian

2016

J. R. Soc. Interface.

236

191

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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.

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“…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).…”

mentioning

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.

440

358

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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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Synthetic gene circuits for metabolic control: design trade-offs and constraints

Cited by 73 publications

References 48 publications

Mechanistic links between cellular trade-offs, gene expression, and growth

Mechanistic links between cellular trade-offs, gene expression, and growth

Control theory meets synthetic biology

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

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