Engineering artificial signalling functions with proteases

Gräwe, Alexander; Ranglack, Jan; Weber, Wadim; Stein, Viktor

doi:10.1016/j.copbio.2019.09.017

Cited by 14 publications

(11 citation statements)

References 49 publications

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“…Given the low level of dependence of such systems on the nature of the dimerization system, it is expected that it is possible to engineer similar systems to a broad range of analytes and biochemical activities. Due to their high specificity and the dramatic changes in the physical properties of their substrates, proteases have attracted significant attention of protein and cellular engineers in the recent years, 11 including the use of proteases in various biosensor systems. 12,14,17,18,27 The present study takes a departure from the designs where the signal-controlled proteolytic reaction activates a zymogen version of the effector polypeptide (for review, see ref 11).…”

Section: ■ Discussionmentioning

confidence: 99%

“…6−10 Among the enzymes capable of generating easily measurable outputs, proteases have a special place due to the dramatic changes in the physical properties of their substrates, high and engineerable substrate specificity, natural orthogonality, and the relative ease of connecting them to diverse protein signaling systems in vivo and in vitro. 11 The examples include the construction of proteaseactivatable autoinhibited signaling modules 12,13 and their integration into ultrasensitive signal amplification circuits. 14 The creation of protease-based artificial receptors and protease-based activated protein reporters 15 enabled the construction of sophisticated and tunable synthetic cellular signaling systems.…”

Section: ■ Introductionmentioning

confidence: 99%

“…This approach holds potential for creating orthogonal signaling systems that connect biochemical networks to nonbiological information processing systems such as electronics, including implantable and wearable bioelectronics. The protein switch engineering efforts have focused on several types of reporter domains: light-emitting proteins such as fluorescent proteins and luciferases, redox enzymes that can be monitored electrochemically, and finally enzymes that can actuate on colorimetric reactions. − Among the enzymes capable of generating easily measurable outputs, proteases have a special place due to the dramatic changes in the physical properties of their substrates, high and engineerable substrate specificity, natural orthogonality, and the relative ease of connecting them to diverse protein signaling systems in vivo and in vitro …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides

et al. 2021

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Enzymatic polypeptide proteolysis is a widespread and powerful biological control mechanism. Over the last few years, substantial progress has been made in creating artificial proteolytic systems where an input of choice modulates the protease activity and thereby the activity of its substrates. However, all proteolytic systems developed so far have relied on the direct proteolytic cleavage of their effectors. Here, we propose a new concept where protease biosensors with a tunable input uncage a signaling peptide, which can then transmit a signal to an allosteric protein reporter. We demonstrate that both the cage and the regulatory domain of the reporter can be constructed from the same peptide-binding domain, such as calmodulin. To demonstrate this concept, we constructed a proteolytic rapamycin biosensor and demonstrated its quantitative actuation on fluorescent, luminescent, and electrochemical reporters. Using the latter, we constructed sensitive bioelectrodes that detect the messenger peptide release and quantitatively convert the recognition event into electric current. We discuss the application of such systems for the construction of in vitro sensory arrays and in vivo signaling circuits.

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Section: ■ Discussionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides

et al. 2021

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“…Several approaches, such as the use of synthetically designed transcription or translation regulators (see e.g. [21,22]), engineered proteases [23] or a decomposition of a logic circuit among different cells in a population can be applied to solve this problem. Decomposition of transcriptional logic to less complex functions distributes the metabolic burden among different cells [2].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, a lot of focus has been devoted to the implementation of logic structures using engineered proteases, which enable us to implement protein-based processing signalling logic [23]. The most recent advances include the construction of split-protease-cleavable orthogonal-coiled coils-based (SPOC) logic circuits [25] and circuits of hacked orthogonal modular proteases (CHOMP) [26].…”

Section: Introductionmentioning

confidence: 99%

A Computational Design of a Programmable Biological Processor

Moškon

Pušnik

Magdevska

et al. 2020

Preprint

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Basic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures are, however, hardly scalable and are yet to be extended to more complex processing structures that would constitute a biological computer.Herein, we make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor, composed of an instruction memory containing a biological program, a program counter that is used to address this memory and a biological oscillator that triggers the execution of the next instruction in the memory. The described processor uses transcription and translation resources of the host cell to perform its operations and is able to sequentially execute a set of instructions written within the so-called instruction memory implemented with non-volatile DNA sequences. The addressing of the instruction memory is achieved with a biological implementation of the Johnson counter, which increases its state after an instruction is executed. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equations-based models. These models can be used to simulate the dynamics of the proposed processor.The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the proposed processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be written manually or can be generated automatically with the employment of the provided compiler.

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Design of a Biohybrid Materials Circuit with Binary Decoder Functionality

Mohsenin,

Wagner,

Rosenblatt

et al. 2024

Advanced Materials

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Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information‐processing circuits into materials. Here, a set of protease‐based biohybrid modules the bioactivity of which can either be induced or inhibited is engineered. Guided by a quantitative mathematical model and following a design‐build‐test‐learn (DBTL) cycle, the modules are wired according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. A 2‐input/4‐output binary decoder for the detection of two small molecules in a material framework that can perform regulated outputs in form of distinct protease activities is designed. The here demonstrated smart material system is strongly modular and can be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.

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Engineering artificial signalling functions with proteases

Cited by 14 publications

References 49 publications

Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides

Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides

A Computational Design of a Programmable Biological Processor

Design of a Biohybrid Materials Circuit with Binary Decoder Functionality

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