Tuning Response Curves for Synthetic Biology

Ang, Jordan; Harris, Edouard A.; Hussey, Brendan J.; Kil, Richard; McMillen, David R.

doi:10.1021/sb4000564

Cited by 155 publications

(169 citation statements)

References 179 publications

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“…• As in [21], an activated gene expression can be modeled through a Hill function. As a consequence, the rate of output protein Out is expressed as…”

Section: A Genementioning

confidence: 99%

“…In the following, we assume to have non-constitutive promoters, i.e. k = 0, which means that there is gene expression only when external activating signals are present [21]. In (5) and hereafter, the square brackets notation stands for protein concentration.…”

Section: A Genementioning

confidence: 99%

“…In (5) and hereafter, the square brackets notation stands for protein concentration. From [21], repression can be obtained by exchanging the roles of K p and In in (5).…”

Section: A Genementioning

confidence: 99%

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A parity check analog decoder for molecular communication based on biological circuits

Marcone

Pierobon

Magarini

2017

IEEE INFOCOM 2017 - IEEE Conference on Computer Communications

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Abstract-Molecular Communication (MC) is an enabling paradigm for the interconnection of future devices and networks in the biological environment, with applications ranging from bio-medicine to environmental monitoring and control. The engineering of biological circuits, which allows to manipulate the molecular information processing abilities of biological cells, is a candidate technology for the realization of MC-enabled devices. In this paper, inspired by recent studies favoring the efficiency of analog computation over digital in biological cells, an analog decoder design is proposed based on biological circuit components. In particular, this decoder computes the a-posteriori log-likelihood ratio of parity-check-encoded bits from a binarymodulated concentration of molecules. The proposed design implements the required L-value and the box-plus operations entirely in the biochemical domain by using activation and repression of gene expression, and reactions of molecular species. Each component of the circuit is designed and tuned in this paper by comparing the resulting functionality with that of the corresponding analytical expression. Despite evident differences with classical electronics, biochemical simulation data of the resulting biological circuit demonstrate very close performance in terms of Mean Squared Error (MSE) and Bit Error Rate (BER), and validate the proposed approach for the future realization of MC components.

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“…• As in [21], an activated gene expression can be modeled through a Hill function. As a consequence, the rate of output protein Out is expressed as…”

Section: A Genementioning

confidence: 99%

Section: A Genementioning

confidence: 99%

See 1 more Smart Citation

A parity check analog decoder for molecular communication based on biological circuits

Marcone

Pierobon

Magarini

2017

IEEE INFOCOM 2017 - IEEE Conference on Computer Communications

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“…One of the most important characteristics of a metabolite biosensor is its ability to discriminate the presence and the absence of its target basal and fully induced states, a dynamic range, could be engineered by generating multiple replications of the entire sensing-actuating process (Ang, Harris, Hussey, Kil, & McMillen, 2013). This approach can amplify the response across the whole range of metabolite concentrations at the same ratio, resulting in the vertical scaling of the dose-response curve.…”

Section: Introductionmentioning

confidence: 99%

Systematic optimization of L‐tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli

Jang

Jung

2017

Biotech & Bioengineering

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Riboswitches form a class of genetically encoded sensor-regulators and are considered as promising tools for monitoring various metabolites. Functional parameters of a riboswitch, like dynamic or operational range, should be optimized before the riboswitch is implemented in a specific application for monitoring the target molecule efficiently. However, optimization of a riboswitch was not straightforward and required detailed studies owing to its complex sequence-function relationship. Here, we present three approaches for tuning and optimization of functional parameters of a riboswitch using an artificial L-tryptophan riboswitch as an example. First, the constitutive expression level was adjusted to control the dynamic range of an L-tryptophan riboswitch. The dynamic range increased as the constitutive expression level increased. Then, the function of a riboswitch-encoded protein was utilized to connect the regulatory response of the riboswitch to another outcome for amplifying the dynamic range. Riboswitch-mediated control of the host cell growth enabled the amplification of the riboswitch response. Finally, L-tryptophan aptamers with different dissociation constants were employed to alter the operational range of the riboswitch.The dose-response curve was shifted towards higher L-tryptophan concentrations when an aptamer with higher dissociation constant was employed. All strategies were effective in modifying the distinct functional parameters of the L-tryptophan riboswitch, and they could be easily applied to optimization of other riboswitches owing to their simplicity. K E Y W O R D Sbiosensor, dose-response curve, L-tryptophan, riboswitch tuning, synthetic biology

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“…Combining multiple markers improves specificity because a weakly active one will buffer the others by thresholding (7,8), as in Boolean logic circuits converting graded inputs into digital-like output (9)(10)(11)(12)(13)(14). The response function of such circuits--input/output activation threshold, amplitude, and sharpness--can be tuned by DNA specificity, promoter design, or protein-protein affinity (15,16).…”

mentioning

confidence: 99%

Cellular heterogeneity mediates inherent sensitivity–specificity tradeoff in cancer targeting by synthetic circuits

Morel

Shtrahman

Rotter

et al. 2016

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

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Synthetic gene circuits are emerging as a versatile means to target cancer with enhanced specificity by combinatorial integration of multiple expression markers. Such circuits must also be tuned to be highly sensitive because escape of even a few cells might be detrimental. However, the error rates of decision-making circuits in light of cellular variability in gene expression have so far remained unexplored. Here, we measure the single-cell response function of a tunable logic AND gate acting on two promoters in heterogeneous cell populations. Our analysis reveals an inherent tradeoff between specificity and sensitivity that is controlled by the AND gate amplification gain and activation threshold. We implement a tumor-mimicking cellculture model of cancer cells emerging in a background of normal ones, and show that molecular parameters of the synthetic circuits control specificity and sensitivity in a killing assay. This suggests that, beyond the inherent tradeoff, synthetic circuits operating in a heterogeneous environment could be optimized to efficiently target malignant state with minimal loss of specificity.synthetic gene circuits | cellular heterogeneity | cancer gene therapy | cell-state targeting | mammalian synthetic biology T he design of gene circuits capable of precisely targeting cancer cells is a major challenge in synthetic biology (1-3), in light of the prospects of using engineered viruses for cancer gene therapy (4), or designing T cells expressing chimeric antigen receptors (CAR-T) (5). Ideally, targeting circuits must be highly sensitive to eradicate all cancer cells, and sufficiently specific to protect surrounding tissues. Gene expression markers that are hyperactive in cancer but not in healthy cells are natural candidates for cancer gene therapy (6). However, a single marker does not suffice because it might be moderately active in normal cells, which would result in incorrect identification. Combining multiple markers improves specificity because a weakly active one will buffer the others by thresholding (7,8), as in Boolean logic circuits converting graded inputs into digital-like output (9-14). The response function of such circuits--input/output activation threshold, amplitude, and sharpness--can be tuned by DNA specificity, promoter design, or protein-protein affinity (15, 16).We previously reported a dual-promoter integrator (DPI) as a logic AND gate to combine the activity of two cancer-specific promoters, and express a reporter or killer gene only when both promoters are decidedly active (17). Subsequently, others used a multiinput logic circuit based on microRNAs to target cancer (18). This Boolean approach provides reliable results on average, but ignores the heterogeneity of cell states. Input values may span a continuum due to expression noise (19,20) and cancer heterogeneity (21). Furthermore, so-called synthetic circuits are not truly digital all-or-none, but rather analog systems that produce continuous signals using transcription factors, expression regulators, and machi...

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Tuning Response Curves for Synthetic Biology

Cited by 155 publications

References 179 publications

A parity check analog decoder for molecular communication based on biological circuits

A parity check analog decoder for molecular communication based on biological circuits

Systematic optimization of L‐tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli

Cellular heterogeneity mediates inherent sensitivity–specificity tradeoff in cancer targeting by synthetic circuits

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