Synthetic biological circuit

Key takeaways

Synthetic biological circuit belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Synthetic biological circuit to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Synthetic biological circuit from memory before moving on to harder problems.

Reference excerpt

Synthetic biological circuits are an application of synthetic biology where biological parts inside a cell are designed to perform logical functions mimicking those observed in electronic circuits. Typically, these circuits are categorized as either genetic circuits, RNA circuits, or protein circuits, depending on the types of biomolecule that interact to create the circuit's behavior. The applications of all three types of circuit range from simply inducing production to adding a measurable element, like green fluorescent protein, to an existing natural biological circuit, to implementing completely new systems of many parts.

The goal of synthetic biology is to generate an array of tunable and characterized parts, or modules, with which any desirable synthetic biological circuit can be easily designed and implemented. These circuits can serve as a method to modify cellular functions, create cellular responses to environmental conditions, or influence cellular development. By implementing rational, controllable logic elements in cellular systems, researchers can use living systems as engineered "biological machines" to perform a vast range of useful functions.

History The first natural gene circuit studied in detail was the lac operon. In studies of diauxic growth of E. coli on two-sugar media, Jacques Monod and Francois Jacob discovered that E.coli preferentially consumes the more easily processed glucose before switching to lactose metabolism. They discovered that the mechanism that controlled the metabolic "switching" function was a two-part control mechanism on the lac operon. When lactose is present in the cell the enzyme β-galactosidase is produced to convert lactose into glucose or galactose. When lactose is absent in the cell the lac repressor inhibits the production of the enzyme β-galactosidase to prevent any inefficient processes within the cell. The lac operon is used in the biotechnology industry for production of recombinant proteins for therapeutic use. The gene or genes for producing an exogenous protein are placed on a plasmid under the control of the lac promoter. Initially the cells are grown in a medium that does not contain lactose or other sugars, so the new genes are not expressed. Once the cells reach a certain point in their growth, isopropyl β-D-1-thiogalactopyranoside (IPTG) is added. IPTG, a molecule similar to lactose, but with a sulfur bond that is not hydrolyzable so that E. coli does not digest it, is used to activate or "induce" the production of the new protein. Once the cells are induced, it is difficult to remove IPTG from the cells and therefore it is difficult to stop expression. Two early examples of synthetic biological circuits were published in Nature in 2000. One, by Tim Gardner, Charles Cantor, and Jim Collins working at Boston University, demonstrated a "bistable" switch in E. coli. The switch is turned on by heating the culture of bacteria and turned off by addition of IPTG. They used green fluorescent protein as a reporter for their system. The second, by Michael Elowitz and Stanislas Leibler, showed that three repressor genes could be connected to form a negative feedback loop termed the Repressilator that produces self-sustaining oscillations of protein levels in E. coli. Currently, synthetic circuits are a burgeoning area of research in systems biology with more publications detailing synthetic biological circuits published every year. There has been significant interest in encouraging education and outreach as well: the International Genetically Engineered Machines Competition manages the creation and standardization of BioBrick parts as a means to allow undergraduate and high school students to design their own synthetic biological circuits.

Interest and goals Both immediate and long term applications exist for the use of synthetic biological circuits, including different applications for metabolic engineering, and synthetic biology. Those demonstrated successfully include pharmaceutical production, and fuel production. However, methods involving direct genetic introduction are not inherently effective without invoking the basic principles of synthetic cellular circuits. For example, each of these successful systems employs a method to introduce all-or-none induction or expression. This is a biological circuit where a simple repressor or promoter is introduced to facilitate creation of the product, or inhibition of a competing pathway. However, with the limited understanding of cellular networks and natural circuitry, implementation of more robust schemes with more precise control and feedback is hindered. Therein lies the immediate interest in synthetic cellular circuits. Development in understanding cellular circuitry can lead to exciting new modifications, such as cells which can respond to environmental stimuli. For example, cells could be developed that signal toxic surroundings and react by activating pathways used to degrade the perceived toxin. To develop such a cell, it is necessary to create a complex synthetic cellular circuit which can respond appropriately to a given stimulus. Given synthetic cellular circuits represent a form of control for cellular activities, it can be reasoned that with complete understanding of cellular pathways, "plug and play" cells with well defined genetic circuitry can be engineered. It is widely believed that if a proper toolbox of parts is generated, synthetic cells can be developed implementing only the pathways necessary for cell survival and reproduction. From this cell, to be thought of as a minimal genome cell, one can add pieces from the toolbox to create a well defined pathway with appropriate synthetic circuitry for an effective feedback system. Because of the basic ground up construction method, and the proposed database of mapped circuitry pieces, techniques mirroring those used to model computer or electronic circuits can be used to redesign cells and model cells for easy troubleshooting and predictive behavior and yields.

Example circuits

Oscillators Repressilator Mammalian tunable synthetic oscillator Bacterial tunable synthetic oscillator Coupled bacterial oscillator Globally coupled bacterial oscillator Elowitz et al. and Fung et al. created oscillatory circuits that use multiple self-regulating mechanisms to create a time-dependent oscillation of gene product expression.

… excerpt ends here. Continue reading the full article.

Illustrations

Synthetic biological circuit: A ribosome is a biological machine. — A ribosome is a biological machine.

Synthetic biological circuit: The logical AND gate.[15][16] If Signal A AND Signal B are present, then the desired gene product will result. All promoters shown are inducible, activated by the displayed gene product. Each signal activates expression of a separate gene (shown in light blue). The expressed proteins then can either form a complete complex in cytosol, that is capable of activating expression of the output (shown), or can act separately to induce expression, such as separately removing an inhibiting protein and inducing activation of the uninhibited promoter. — The logical AND gate.[15][16] If Signal A AND Signal B are present, then the desired gene product will result. All promoters shown are inducible, activated by the displayed gene product. Each signal activates expression of a separate gene (shown in light blue). The expressed proteins then can either form a complete complex in cytosol, that is capable of activating expression of the output (shown), or can act separately to induce expression, such as separately removing an inhibiting protein and inducing activation of the uninhibited promoter.

Synthetic biological circuit: The logical OR gate.[15][16] If Signal A OR Signal B are present, then the desired gene product will result. All promoters shown are inducible. Either signal is capable of activating the expression of the output gene product, and only the action of a single promoter is required for gene expression. Post-transcriptional regulation mechanisms can prevent the presence of both inputs producing a compounded high output, such as implementing a low binding affinity ribosome binding site. — The logical OR gate.[15][16] If Signal A OR Signal B are present, then the desired gene product will result. All promoters shown are inducible. Either signal is capable of activating the expression of the output gene product, and only the action of a single promoter is required for gene expression. Post-transcriptional regulation mechanisms can prevent the presence of both inputs producing a compounded high output, such as implementing a low binding affinity ribosome binding site.

Synthetic biological circuit: The logical Negated AND gate.[15][16] If Signal A AND Signal B are present, then the desired gene product will NOT result. All promoters shown are inducible. The activating promoter for the output gene is constitutive, and thus not shown. The constitutive promoter for the output gene keeps it "on" and is only deactivated when (similar to the AND gate) a complex as a result of two input signal gene products blocks the expression of the output gene. — The logical Negated AND gate.[15][16] If Signal A AND Signal B are present, then the desired gene product will NOT result. All promoters shown are inducible. The activating promoter for the output gene is constitutive, and thus not shown. The constitutive promoter for the output gene keeps it "on" and is only deactivated when (similar to the AND gate) a complex as a result of two input signal gene products blocks the expression of the output gene.

Worked examples

Example 1 — a first encounter with Synthetic biological circuit

Start with the simplest possible case. Write down what Synthetic biological circuit claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Synthetic biological circuit before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Synthetic biological circuit ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Synthetic biological circuit

In research: Synthetic biological circuit appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Synthetic biological circuit in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Synthetic biological circuit is common in secondary-school and first-year university syllabi. It links to neighbouring topics Synthetic biology, so understanding it makes those chapters shorter.
In everyday life: Look for Synthetic biological circuit outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study Synthetic biological circuit in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Synthetic biological circuit means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Synthetic biological circuit out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Synthetic biological circuit in simple terms?

Synthetic biological circuits are an application of synthetic biology where biological parts inside a cell are designed to perform logical functions mimicking those observed in electronic circuits. Typically, these circuits are categorized as either genetic circuits, RNA circuits, or protein circui…

Why does Synthetic biological circuit matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Synthetic biological circuit?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Synthetic biological circuit.