Peking 2018 joined the fifth Interlab measurement study. This year we helped to answer this question: Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?
To design multivalent modules, it is not ideal to use multiple repeat domains, which not only will make the protein extremely large and bring difficulties to DNA recombination, but also may be problematic for making transgenic animals. Thus, instead of using multiple repeats, we turned to de novo-designed homo-oligomeric coiled coils. And we named these coiled coils as HO-Tag (homo-oligomeric tag). They are short peptides, ~30 amino acids[1], therefore they are ideal tags to introduce multivalency. There are seven coiled coils previously characterized in protein de novo design studies. They have been proved by previous work of Shu Xiaokun’s lab, and according to their work, HOTag3 and HOTag6 are most robust in driving protein droplet formation over a wide range of protein concentrations, so we choose them.
To design interaction modules, we tried a lot of components and we fused them to the N-terminus of HOTag3 or HOTag6. Some of them are spontaneous and some are inducible. And we can regulate them through various kinds of inducers and different intensities of promoters.
Post-translational modifications by the small ubiquitin-like modifier (SUMO) are crucial events in cellular response to radiation and a wide range of DNA-damaging agents. Previous studies have shown that SUMO mediates protein-protein interactions by binding to a SUMO-interacting motif (SIM) on receptor proteins. And recent studies have shown that a protein with ten repeats of human SUMO3 (polySUMO) and a protein with ten repeats of SIM (polySIM) can phase separate in vitro[3]. Therefore, we chose SUMO3 and SIM as a pair of interaction modules and they can drive the formation of synthetic organelles spontaneously. For plasmid construction, in order to make synthetic organelles visible, we chose mCherry (red fluorescent protein) and yEGFP (yeast-enhanced green fluorescent protein) as reporters. Then, we fused mCherry between the C-terminus of SIM and the N-terminus of HOTag6. Similarly, we fused yEGFP between the C-terminus of SUMO and the N-terminus of HOTag3. We transformed them into yeast and proved that they can stably express. If it work, we will find red granules colocalize with green granules in cells under fluorescence microscope.
The interaction between FKBP and FRB can be robustly induced by rapamycin. Rapamycin is a 31-membered macrolide antifungal antibiotic. It binds with high affinity (Kd=0.2nM) to the 12-kDa FK506 binding protein (FKBP), as well as to a 100-amino acid domain of the mammalian target of rapamycin (mTOR) known as FKBP-rapamycin binding domain (Frb)[5]. Thus, we chose them as a pair of interaction modules. And we assembled them on to yeast plasmid as the same as the construction of SUMO and SIM and transformed them into yeast. if we add rapamycin to the yeast, we will see red granules colocalize with green granules in cells under fluorescence microscope. Synthetic organelles come true!
As mentioned above, interactions can be formed not only by inducers such as rapamycin and gibberellin, but also spontaneously, just as SUMO and SIM. So can we combine these two ways of interactions? To solve this problem, we did further studies about phytohormone and found ABA. Abscisic acid (ABA) is an important phytohormone that regulates plant stress responses. Proteins from the PYR-PYL-PCAR family were identified as ABA receptors[6]. Upon binding to ABA, a PYL protein associates with type 2C protein phosphatases (PP2Cs) such as ABI1 and ABI2, inhibiting their activity[7]. Previous structural and biochemical observations have provided insight into PYL-mediated ABA signaling and given rise to a working model. In the absence of ABA signaling, PP2Cs are fully active and PYLs exist as inactive homodimers in cells, unable to bind or inhibit PP2Cs, mainly due to the incompatible conformation of CL2loop[7]. In response to ABA binding, the CL2 loop undergoes a conformational rearrangement to close onto the ABA-bound pocket, then, the interaction between PYLs and PP2Cs can be formed. Here we chose PYL1 and ABI1 as a pair of interaction modules. Then, we assembled them on to yeast plasmid as the same as the construction of FKBP and FRB and transformed them into yeast. Based on the interaction of PYL1 and ABI1, we can get a wonderful scene: In the absence of ABA, the synthetic organelles composed only of PYL1 appear, because of the homodimers of PYL1. And after we add ABA into yeast, ABI1 can enter the organelles with the interaction of ABI1 and PYL1, and we can see red droplets colocalize with green droplets in cells through fluorescence microscope. In this way, new components can enter the original organelles and the time of occurrence can be regulated as it is inducer-mediated regulation. So it give our designs and functions more possibilities.
Now, we have artificially designed phase separation in cells and synthesized membraneless organelles. But how can we fulfill intended functions with synthetic organelles? Here, we propose two ideas. We reserve two sites to implement functions, which means function modules, such as enzymes in metabolism, proteins in signaling pathway, transcription factors in transcription and so on, have two sites in our designs.
Just as we characterize synthetic organelles with fluorescent proteins, we can fuse function modules to the C-terminus of interaction modules and to the N-terminus of HOTags. Then, the function modules can be “kidnapped” into the synthetic organelles to fulfill intended functions.
We introduce a magic protein, anti-GFP nanobody, which is very small (only 13-kDa, 1.5nm 2.5nm) and high-affinity (0.59nM) camelid antibody to GFP[8]. So we can use its characteristic to improve our designs. We can fuse GFP to the C-terminus of interaction modules and to the N-terminus of HOTags, and fuse function modules to the C-terminus of anti-GFP nanobodies. Then, with the help of interaction between anti-GFP nanobodies and GFP, synthetic organelles will “welcome” function modules, expected functions can be realized. You may ask: How does anti-GFP nanobody improve the design? Firstly, it will not make the protein extremely large and will reduce the effect on the structure of function modules, which can ensure the quality of functions. Secondly, it can bring components not belonging to the original structure to synthetic organelles, which can enlarge the enrichment range of synthetic organelles. Thirdly, it is easy to regulate the expression of target proteins. So you can see, nanobodies may do better and give you a surprise!
We artificially designed phase separation in cells and synthesized membraneless organelles. And the main work to synthesize an organelle is to fulfill phase separation in a cell, so we stress the importance of interactions and multivalency. For these two aspects, we gave our ideas and the feasibility was analyzed. At last, we proposed two ideas to implement functions. We believe that in the near future, “millions of dollars” will no longer be a dream!
[1] Zhang, Q., Huang, H., Zhang, L., Wu, R., Chung, C. I., Zhang, S. Q., ... & Shu, X. (2018). Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter. Molecular cell, 69(2), 334-346.
[2] Woolfson, D. N., Bartlett, G. J., Burton, A. J., Heal, J. W., Niitsu, A., Thomson, A. R., & Wood, C. W. (2015). De novo protein design: how do we expand into the universe of possible protein structures?. Current opinion in structural biology, 33, 16-26.
[3] Banani, S. F., Rice, A. M., Peeples, W. B., Lin, Y., Jain, S., Parker, R., & Rosen, M. K. (2016). Compositional control of phase-separated cellular bodies. Cell, 166(3), 651-663.
[4] Husnjak, K., Keiten-Schmitz, J., & Müller, S. (2016). Identification and characterization of SUMO-SIM interactions. In SUMO (pp. 79-98). Humana Press, New York, NY.
[5] Banaszynski, L. A., Liu, C. W., & Wandless, T. J. (2005). Characterization of the FKBP Rapamycin FRB Ternary Complex. Journal of the American Chemical Society, 127(13), 4715-4721.
[6] Park, S. Y., Fung, P., Nishimura, N., Jensen, D. R., Fujii, H., Zhao, Y., ... & Alfred, S. E. (2009). Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. science, 324(5930), 1068-1071.
[7] Yin, P., Fan, H., Hao, Q., Yuan, X., Wu, D., Pang, Y., ... & Yan, N. (2009). Structural insights into the mechanism of abscisic acid signaling by PYL proteins. Nature structural & molecular biology, 16(12), 1230.
[8] Ries, J., Kaplan, C., Platonova, E., Eghlidi, H., & Ewers, H. (2012). A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nature methods, 9(6), 582.
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