Difference between revisions of "Team:Peking/Project"

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                             <li class="dropdown menu-3"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Modeling</a>
 
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                                     <li><a href="https://2018.igem.org/Team:Peking/Model">Overview</a></li>
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                                     <li><a href="https://2018.igem.org/Team:Peking/Project_overview">Overview</a></li>
 
                                     <li><a href="https://2018.igem.org/Team:Peking/SPOT_Formation" class="barfont1">SPOT Formation</a></li>
 
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                                     <p>Ever since the beginning of life, compartment has been playing a crucial rule in biological systems. The famous Miller-Urey experiment shows that inorganic molecules can transform into organic substances under extreme conditions, for example lightening. However, homogeneously distributed organic matters are not enough for life to emerge. It is almost impossible that all conditions are proper in the entire primordial soup.
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                                     <p>We believe that our work has reached the medal requirements of demonstration as we have confirmed that our synthetic organelles can be formed in vivo and deliver a range of functions both for engineering and research due to their amazing properties. The concrete demonstration of the whole platform is shown below. You can see more details of experiments and modeling in our <a href="https://2018.igem.org/Team:Peking/Results"/>Data Page</a> and <a href="https://2018.igem.org/Team:Peking/Model"/>Modeling</a></p><br/><br/><br/>       
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That is where the compartment comes in.
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Only after coacervate droplet forms and organic molecules condense inside, a completely different environment can be attained within, thus enabling the emergence of bio-macromolecules, or in other word, making life possible.
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In cells, compartmentalization is mainly achieved be all sorts of organelles, for instance, mitochondrion, chloroplast, lysosome etc. They take up three major roles: A, B, C
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Intuitively, for a organelle to sustain a stable compartment, it seems necessary to require a material boundary, more precisely, a membrane. Membrane-bound organelles are indeed common and stable, but from the perspective of synthesis, it is way too complicated. However, there are also non-membrane-bound organelles, for instance, stress granule, P granule and nucleolus. More importantly, their formation is guided by simple physical principals.
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Then came the question that how can we synthase membraneless organelles. The process where material self-assemble into organelles is described as ‘phase separation’ according to physical chemistry, which is the conversion of a single-phase system into a multiphase system, much like how oil and water will demix from each other. In general, materials flow to regions with low chemical potential instead of low concentration. Finally, the components no longer distribute uniformly but form granules locally which are organelles in the cell.
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(图片2)
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That is to say, the main work to synthase an organelle is to fulfill phase separation in a cell. We take our inspiration from existing life systems. For example, stress granules and P bodies are formed by the interaction between mRNA and proteins. RNA and protein play a significant part in the phase separation in cells. IDR(Intrinsic Disordered Regions) are the symbol of massive phase separation in the cell. IDR interact with each other through the van der Waals force, electrostatic effect and hydrophobic effect between the residues of amino acids, while RNA get together with proteins through massive bases and ribose. Previous work has been done to reproduce natural phase separation by connecting interaction modules like SUMO/SIM, SH3/PRM, constructing granules in the cell.
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(图片4)
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Summarizing these examples and according to physical principles, interaction between modules and multivalence are essential for phase separation. In general, interaction binds the parts together and multivalence makes larger assemblies, which are two guidance of our design.
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(图片5 )
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<div class="texttitle">Phase Separation System
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                                    <div class="ordi">1.</div>
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                                    <h3>Spontaneous and induced synthetic organelles can be formed by phase separation</h3>
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                                    <p>Our basic system consists of two components of synthetic organelles. Either of them has a specific HOtag to form homo-oligomers. We expect that they are able to form synthetic organelles due to the principles of phase separation. To verify the feasibility of the design, we fused two fluorescence proteins with the two components of synthetic organelles (Figure1.a) so that we can observe the self-organization of components and the formation of granules under fluorescence microscope.</p>
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                                    <p>We used SUMO-SIM interaction module to build a spontaneous organelle. When two components are expressed in yeasts, granules with the two fluorescence proteins can be observed in vivo (Figure1.b). </p>
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                                    <p>Meanwhile, by rapamycin induced interaction module, FKBP-Frb, we have built an inducible organelle. We can see granules occurs in yeasts within minutes after adding the inducer.</a> </p>
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Figure1.a The basic design of synthetic organelles with florescence reporters. <img src="https://static.igem.org/mediawiki/2018/3/36/T--Peking--Logo.png" style="width:100%;" alt="">（这里可能需要一张cartoon的设计图）
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            b, c fluorescence images of spontaneous organelles (SUMO-SIM based) and inducible synthetic organelles (FKBP-Frb based, after adding 10000 nM rapamycin)<br/><br/>
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                                    <div class="ordi">2.</div>
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                                    <h3>The formation of organelles has flexible but predictable properties and kinetics in different conditions</h3>
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                                    <p>Then we combined <a href="https://2018.igem.org/Team:Peking/Phase_Separation_M"/>modeling of phase separation</a> and experiment to research the kinetics of the organelles formation process expecting that a well-characterized system can reach its whole potential in complex applications. </p>
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                                    <p>As the model predicts, the concentration of components and the interaction strength affect the kinetics of phase separation. First we controlled the expression levels of components by using several stable or inducible promoters and observe the system's behavior. We found that the formation of organelles happened in specific promoter combinations and can be controlled by inducible promoters. The analysis result does not only fit well with the simulation, but provides potential methods to control the organelles in applications. </p>
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Figure2 (a) Phase diagram of a phase separation system with three components(simulation). To fit our system, the x-axis and the y-axis stands for the two components in the granules. The asymmetry comes from the assumption that the two components have different interactions with water.
 +
(b) Fluorescence movies of different promoter combinations of FKBP-Frb mediated system after adding rapamycin. Only in specific combinations, synthetic organelles can be formed by phase separation.
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(c) The formation process of SUMO-SIM mediated synthetic organelles can be controlled by inducible promoters. While the expression of Tet07-SIM-mCherry-HoTag6 is induced by dox gradually, the granules will occur abruptly in some time.<br/><br/>
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                                    <p>The strength of interaction modules can be also controlled. In the rapamycin-induced organelle system, changing the concentration of rapamycin will affect the apparent value of K, a parameter reflecting the interaction strength in our model. In a gradient rapamycin-inducing experiment, the delay time from adding inducer to granules formation was found to be shorter when concentration of rapamycin increases. So we have confirmed the influence of two parameters in models and increased the flexibility of our synthetic organelles.</p>
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Figure3 (a) A simulation of organelle formation process in different interaction strength of components.
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(b) The speed of FKBP-Frb mediated organelle formation increases with the increasing concentration of rapamycin.
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                                    <p>We also tried to characterized other properties, like the liquid-like property of the synthetic organelles, as they may affect the functions. See more details about our characterizations in <a href="https://2018.igem.org/Team:Peking/Phase_Separation_D"/>DataPage Phase separation</a>.</p><br/><br/><br/>
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                            <div class="texttitle">Functional Organelles
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                                    <p>Since SPOT can form in the cell and be controlled, we go further to consider the functions of SPOT. The functions of SPOT can be descripted in three catalogs: Spatial segmentation, Sensor and metabolic regulation. We verified the spatial segmentation with the condensation of substrates, also we can load the protein we want by fusing it with nanobody. We then verified the sensor with detecting rapamycin and ABA, which shows strong relativity between the concentration and the proportion of yeasts with SPOT. To find the law behind metabolism in the SPOT, we fuse the enzymes that can produce β-carotene into SPOT and measure the difference between with or without SPOT in produce of β-carotene.</p>
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Figure4 (organization hub)
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Design of GFP-nanobody based system
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fluorescence images of GFP-nanobody based system
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Figure5 (sensor)
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(a)~(?) fluorescence images of sensor based system
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Figure6 (metabolism)
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Characterization of carotene production system
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（phase内和phase外的胡萝卜素生产实验）<br/><br/><br/><br/><br/>
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                            <div class="texttitle">Perspective
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                                    <p>SPOT has been well verified and has various functions. And in the future, this modular system will have great potential in science and practice using. SPOT can change the modules to gain more different properties like diverse inducing method, we can also use it as a platform and then load other protein with some interactions like the interaction between nanobody and GFP. What’s more, we might have the ability to form differernt SPOTs in the cell and regulate them respectively. The functions of SPOT can also diverse. We can build a real time sensor for molecule in living cells to monitoring the concentration changing in environment or in cells. More metabolism pathway can be test in SPOT and we will find some laws of the function of regulate the metabolism. To be summary, more achievement is coming true with SPOT.</p>
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Revision as of 15:05, 14 October 2018

Description

In this section, you could see the demonstration.

Overview

The aim of our project is to build a synthetic organelle based on phase separation as a multifunctional platform. Based on the principle of multivalence and interaction, we fused interactional modules into homo-oligomeric tags (HOtags) to form granules in S. cerevisiae.

We have built spontaneous and induced synthetic organelles by specific interaction modules, so that we can control the formation process by different ways for demands in biological engineering. Then we characterized the kinetics and properties of synthetic organelles theoretically and experimentally. These results confirm the potential of synthetic organelles in synthetic biology.

It inspired us to propose some specific applications of our synthetic organelles, including organization hub, sensor, and metabolism regulator. We have verified the feasibility of them by loading GFP-nanobody module, NAD+ sensor module and carotene production module to the whole system.

We believe that our work has reached the medal requirements of demonstration as we have confirmed that our synthetic organelles can be formed in vivo and deliver a range of functions both for engineering and research due to their amazing properties. The concrete demonstration of the whole platform is shown below. You can see more details of experiments and modeling in our Data Page and Modeling




Phase Separation System
1.

Spontaneous and induced synthetic organelles can be formed by phase separation

Our basic system consists of two components of synthetic organelles. Either of them has a specific HOtag to form homo-oligomers. We expect that they are able to form synthetic organelles due to the principles of phase separation. To verify the feasibility of the design, we fused two fluorescence proteins with the two components of synthetic organelles (Figure1.a) so that we can observe the self-organization of components and the formation of granules under fluorescence microscope.

We used SUMO-SIM interaction module to build a spontaneous organelle. When two components are expressed in yeasts, granules with the two fluorescence proteins can be observed in vivo (Figure1.b).

Meanwhile, by rapamycin induced interaction module, FKBP-Frb, we have built an inducible organelle. We can see granules occurs in yeasts within minutes after adding the inducer.

Figure1.a The basic design of synthetic organelles with florescence reporters. （这里可能需要一张cartoon的设计图） b, c fluorescence images of spontaneous organelles (SUMO-SIM based) and inducible synthetic organelles (FKBP-Frb based, after adding 10000 nM rapamycin)

2.

The formation of organelles has flexible but predictable properties and kinetics in different conditions

Then we combined modeling of phase separation and experiment to research the kinetics of the organelles formation process expecting that a well-characterized system can reach its whole potential in complex applications.

As the model predicts, the concentration of components and the interaction strength affect the kinetics of phase separation. First we controlled the expression levels of components by using several stable or inducible promoters and observe the system's behavior. We found that the formation of organelles happened in specific promoter combinations and can be controlled by inducible promoters. The analysis result does not only fit well with the simulation, but provides potential methods to control the organelles in applications.


Figure2 (a) Phase diagram of a phase separation system with three components(simulation). To fit our system, the x-axis and the y-axis stands for the two components in the granules. The asymmetry comes from the assumption that the two components have different interactions with water. (b) Fluorescence movies of different promoter combinations of FKBP-Frb mediated system after adding rapamycin. Only in specific combinations, synthetic organelles can be formed by phase separation. (c) The formation process of SUMO-SIM mediated synthetic organelles can be controlled by inducible promoters. While the expression of Tet07-SIM-mCherry-HoTag6 is induced by dox gradually, the granules will occur abruptly in some time.

The strength of interaction modules can be also controlled. In the rapamycin-induced organelle system, changing the concentration of rapamycin will affect the apparent value of K, a parameter reflecting the interaction strength in our model. In a gradient rapamycin-inducing experiment, the delay time from adding inducer to granules formation was found to be shorter when concentration of rapamycin increases. So we have confirmed the influence of two parameters in models and increased the flexibility of our synthetic organelles.


Figure3 (a) A simulation of organelle formation process in different interaction strength of components. (b) The speed of FKBP-Frb mediated organelle formation increases with the increasing concentration of rapamycin.

We also tried to characterized other properties, like the liquid-like property of the synthetic organelles, as they may affect the functions. See more details about our characterizations in DataPage Phase separation.




Functional Organelles

Since SPOT can form in the cell and be controlled, we go further to consider the functions of SPOT. The functions of SPOT can be descripted in three catalogs: Spatial segmentation, Sensor and metabolic regulation. We verified the spatial segmentation with the condensation of substrates, also we can load the protein we want by fusing it with nanobody. We then verified the sensor with detecting rapamycin and ABA, which shows strong relativity between the concentration and the proportion of yeasts with SPOT. To find the law behind metabolism in the SPOT, we fuse the enzymes that can produce β-carotene into SPOT and measure the difference between with or without SPOT in produce of β-carotene.

Figure4 (organization hub) Design of GFP-nanobody based system fluorescence images of GFP-nanobody based system Figure5 (sensor) (a)~(?) fluorescence images of sensor based system Figure6 (metabolism) Characterization of carotene production system （phase内和phase外的胡萝卜素生产实验）




Perspective

SPOT has been well verified and has various functions. And in the future, this modular system will have great potential in science and practice using. SPOT can change the modules to gain more different properties like diverse inducing method, we can also use it as a platform and then load other protein with some interactions like the interaction between nanobody and GFP. What’s more, we might have the ability to form differernt SPOTs in the cell and regulate them respectively. The functions of SPOT can also diverse. We can build a real time sensor for molecule in living cells to monitoring the concentration changing in environment or in cells. More metabolism pathway can be test in SPOT and we will find some laws of the function of regulate the metabolism. To be summary, more achievement is coming true with SPOT.