Team:HZAU-China/Project

1. Overview

Cells sense the environment, process information, and make response to stimuli. To make cells work well in complex natural environments, lots of processes have to be preset to react to various signals. However, when well-characterized modules are combined to construct higher order systems, unpredictable behaviors often occur because of the interplay between modules. Another significant problem is that complex integrated systems composed of numerous parts may cause cell overload.

We proposed an elegant method to design higher order systems. Instead of merely combining different functional modules, we constructed one integrated processing module with fewer parts by utilizing the common structures between modules. The circuit we designed is a rewirable one and the topological structure of the processing module can be altered to adapt to environmental change. The basic idea is to rewire the connections between parts and devices to implement multiple functions with the help of the site-specific recombination systems.

Based on the design principle we put forward, we built two circuits to verify our idea. Each circuit has three modules including an input module, a processing module, and an output module. The input module receives environmental signal and triggers the rewiring of the processing module. The output module monitors real-time processes using fluorescence intensity.

Our design approach may lead to a revolutionary step towards system integration in synthetic biology. Potential fields of application include organism development, living therapeutics and environment improvement.

2. Background

Since its inception more than a decade ago, synthetic biology has undergone considerable development and has attained significant achievements with the help of the engineering slant. However, there are still obstacles to build a cell. Engineers try to abstract the DNA sequences into some standard functional parts and assemble them using some principles in electrical engineering. So far, the limited understanding of biological system prevents them to combine parts and modules to create larger scale systems. The complexity of synthetic systems didn’t increase rapidly as the Moore’s law (Purnick and Weiss, 2009).

Challenges

There are some common problems that make the circuits we designed not work as our expected. Many failure modes have been collated by Brophy and Voigy in their review (Brophy and Voigt, 2014). In our project, we mainly focus on two modes, crosstalk and host overload, that emerge especially when we create more sophisticated systems. More specifically, regulators may interact with each other’s targets leading to errors in the desired operation, and the synthetic circuits may compete with natural parts that maintain the normal cellular processes for limited resources.

Solution

We design a time-sharing system that can process information according to the input signal. Cells rewire its synthetic circuit to alter the topological structure of regulatory pathway when they receive the corresponding stimuli. In this way, we reuse the existing synthetic module rather than add a new one to implement another function, which reduces the resource cost in running unnecessary function and the interplay between parallel modules. After overcoming these two big problems, our engineered cells are more versatile and flexible in information processing.

3. Input Module

The input module is in charge of the expression of recombinase according to the received signals. When there’s no input signal, there is leaky expression. Such leakage may unexpectedly alter the function of the processing module. So we need tighter regulation. We cloned the recombinase under the control of the inducible riboregulators (Callura et al., 2012; Bonnet et al., 2013).

Site-specific recombination

The site-specific recombination system we used in our project is Cre recombinase meditated inversion system. We chose two mutant loxP sites, lox66 and lox71, instead of the wild-type loxP sites. After the first Cre-mediated recombination, one wild-type loxP site and one double mutant loxP site are generated. The double mutant loxP site, lox72, exhibits a very low affinity for Cre recombinase. So it can be regarded as a unidirectional one, or an irreversible one.

Riboregulator

In a riboregulator, the cis-repressed RNA is like a lock, and the trans-activating RNA is like a key. When they reach a certain concentration, the trans-activating RNA is designed to target and hybridize to the stem-loop of the crRNA message. The resulting RNA duplex causes a conformational change in the crRNA that unfolds the stem-loop, exposing the RBS and permitting translation. In this way we can achieve a post-transcriptional control.

Coherent feedforward loop

We incorporated a coherent feedforward loop into our input module. This motif can provide pulse filtration in which short pulses of signal will not generate a response but persistent signals will generate a response after short delay. So we utilized this property to filter noise.

4. Processing Module

Motivation

Many engineered cells that worked well in a laboratory environment didn’t work well in complex natural environments. Natural cell can adapt to the environment since they have a hierarchical regulatory network. So we want to integrate multiple processing functions in our engineered cells. Taking the limited resources in cells into account, we construct one integrated processing module with fewer parts by utilizing the common structures between modules, instead of merely combining different functional modules.

How we design

We put forward a concept of rewirable circuit. The topological structure of regulatory pathway can be modified to adapt to environmental change. First, we constructed a transcription regulatory pathway by combining inducible promoters and corresponding regulators. Besides, we added some special sequences into the synthetic circuit. These sites can be recognized by recombinase protein and help to rearrange the parts connection by site-specific recombination. After the rearrangement, the circuit we designed is rewired to achieve another function.

We use two examples to demonstrate our idea, and we will describe the general steps about how to design rewirable circuits in the modeling part.

In design 1, the processing module is similar to the classic repressilator, which is composed of three NOT gates. cI represses tetR, which represses lacI, which represses cI. What's different is that the transcription directions of these three genes in our design are no longer the same as that in the classic repressilator. This is because we want to put two promoters more closely. And we add a pair of reversed lox sites on either side of the promoters (Fig. 1).

Figure 1. Circuit in design 1

After rewiring the circuit, the regulatory relationship among these three genes is altered. It is now cI that represses lacI. So cI and lacI inhibit each other. And the repressilator which is composed of three NOT gates is rewired to be a toggle switch composed of two NOT gates(Fig. 2).

Figure 2. Abstract structure in design 1

In design 2, the parts we used are from a quorum sensing system. When the signal molecule AHL binds to luxR proteins, it activates the luxpR promoter and represses the luxpL promoter. LuxI synthesizes more AHL and AiiA contributes to the degradation of AHL. We used luxpR promoter to express luxI and used luxpL promoter to express AiiA (Fig. 3). Then a direct positive feedback loop and an indirect positive feedback loop formed (Fig. 4). When the inversion happens, it’s now luxpR that will express AiiA and it's luxpL that will express luxI (Fig. 3). So now more AHL will repress its own production, and will activate its own degradation. And this is a negative feedback loop (Fig. 4).

Figure 3. Circuit in design 2

Figure 4. Abstract structure in design 2

5. Output Module

In the first stage, the output module is the fluorescent indicator that can monitor the real-time processes of our system. Once its function is confirmed, we can use other functional parts as output to solve real world problems.

RNA level fluorescence

Beside fluorescent proteins, we try to use an RNA-fluorophore complex (Paige et al., 2011) to monitor the real-time processes. The complex contains RNA aptamers and some corresponding fluorophores. We synthesized the fluorophore 3,5-dimethoxy-4-hydroxybenzylidene imidazolinone (DHMBI), because several aptamers were identified that exhibited markedly different spectral properties when they bound to DHMBI. We also synthesized the 13-2min sequence, one of the aptamers that can interact with DHMBI, with a modified tRNA scaffold, which can stabilized the structure.

Figure 5. The resulting image under the fluorescent microscope

6. Application

Multiple functions integration

Multiple functions integration is the general goal we want to achieve. As the number of system components grows, it becomes increasingly difficult to coordinate component inputs and outputs to produce the overall desired behavior. For this reason, we increase the complexity of the system by reusing the exist parts instead of addition of new parts. Our design allows the cells to run different functions at different time and it will not give extra burden to cells when a function is unnecessary.

Organism development

Many researches understand what orchestrates epigenomic changes by Waddington’s model of epigenetic determination of development (Fig. 6) (Mohammad and Baylin, 2010). From a dynamic view, the organism development is like jumping among different attractors. Once the cell falls into a stable steady state, it will be very hard to jump out. Many motifs in developmental network like mutual inhibition and double-positive feedback loop exhibit irreversibility unless the environment has a big change. If the gene circuit that decides the cell fate were rewirable, we could easily reprogram the cell.

Figure 6. Depiction of potential cell signaling in Waddington's model of epigenetic determination of development

Living therapeutics

The tumor suppressor p53 can induce cell cycle arrest or apoptosis according to degree of DNA damage. It was reported that p53 and its downstream targets applied an oscillation mode to repair DNA damage and chose a bistability mode to trigger apoptosis once the damage cannot be fixed by oscillation mode (Zhang et al., 2011). These functions were achieved by a very complex systems (Fig. 7).

Figure 7. A complex mechanism described in previous study

In our design, we can achieve these functions by using only three genes and rewiring their regulatory pathway. We can construct an oscillation into the therapeutic bacterium that colonizes a niche in the human microbiome to maintain homeostasis. And once the the equilibrium is broken, the oscillation will be rewired to be a switch used for next decision.

Environment improvement

Some environment projects in synthetic biology utilize an event trigger to keep expressing some special proteins to tackle the environmental problem. These systems often contain a positive feedback loop module that can memorize the received signal and activate the downstream functional protein. After the problem is handled, we don’t need the positive feedback module anymore, but it is difficult to stop this module. In this case, we can rewire the system rather than kill all these meritorious cells. The positive feedback module can be rewired to be a negative feedback module, which is used to maintain the lower steady state or control the population of the engineered cells. Once the environmental problem recurs, we will rewire it to be a positive feedback one again.

References

Purnick, P. E., & Weiss, R. (2009). The second wave of synthetic biology: from modules to systems. Nature reviews Molecular cell biology, 10(6), 410-422.

Brophy, J. A., & Voigt, C. A. (2014). Principles of genetic circuit design. Nature methods, 11(5), 508-520.

Siuti, P., Yazbek, J., & Lu, T. K. (2013). Synthetic circuits integrating logic and memory in living cells. Nature biotechnology, 31(5), 448-452.

Callura, J. M., Cantor, C. R., & Collins, J. J. (2012). Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences, 109(15), 5850-5855.

Paige, J. S., Wu, K. Y., & Jaffrey, S. R. (2011). RNA mimics of green fluorescent protein. Science, 333(6042), 642-646.

Mohammad, H. P., & Baylin, S. B. (2010). Linking cell signaling and the epigenetic machinery. Nature biotechnology, 28(10), 1033-1038.

Zhang, X. P., Liu, F., & Wang, W. (2011). Two-phase dynamics of p53 in the DNA damage response. Proceedings of the National Academy of Sciences,108(22), 8990-8995.