Deciphering the architecture of multiphasic biomolecular condensates

Taranpreet Kaur’s interview with Bio Patrika hosting “Vigyan Patrika”, a series of author interviews. Taranpreet is currently a research assistant and working towards her Ph.D. in Dr. Priya Banerjee’s lab at the Department of Physics, SUNY Buffalo, NY. Her research focuses on biophysical methods to characterize biomolecular condensates/ Membrane-less organelles, spontaneously formed by Intrinsically disordered proteins and Nucleic Acids. She is from Ludhiana, Punjab, India, and completed her Master’s degree in Physics from Panjab University, Chandigarh. She is a confused physicist in the exciting but complex world of biology, who loves singing and dancing when she is not doing experiments. Here, Taranpreet talks about her work titled ” Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies ” published as the first author in Nature Communications (2021).

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How would you explain your paper’s key results to the non-scientific community?

Cells, the basic building blocks of all living systems, use compartments to segregate their molecular components and their associated biochemical processes. Typically, the compartments/organelles have membranes that help separate their content from the surrounding cellular environment. However, a certain class of organelles can achieve similar segregation without the presence of an enveloping membrane. Their complete isolation from the surrounding media is thought to occur via a well-known process in polymer physics called liquid-liquid phase separation. In simple words, these organelles are perceived to separate from the cellular milieu in a similar manner as the oil/vinegar droplets spontaneously separate from water. At the molecular level, the phase separation process is achieved via multivalent proteins and nucleic acids that condense together to give rise to these membraneless organelles (also called biomolecular condensates).

Figure 1. Schematic representation of architecture of multiphasic biomolecular condensates with increasing concentration of RNA.

Beyond a simple segregation tool, these condensates act as reaction crucibles to tune biochemical reactions and storage compartments for cells under conditions of stress. Interestingly, many different types of biomolecular condensates, such as stress granules and processing bodies coexist in the cell without mixing. Studies have shown that these condensates can organize themselves in diverse patterns, such as attached condensates, detached condensates, or nested condensates where one resides within another. Given these varied patterns of condensates may control their biological functions, our present study focused on elucidating the physical mechanisms behind these different patterns of coexisting biomolecular condensates. Using a tractable model system composed of two proteins and one RNA, we show two mechanisms by which we could regulate the structuring of two coexisting condensates. Evidently, the coexistence pattern between two different condensates is dependent on the favorability of interaction at the condensates’ surfaces. We found that the presence of surface interactions promoted the nested condensate pattern, while the absence of such interactions promotes the detachment of the two condensates from each other. The surface interaction can be controlled, as we show, via two pathways – 1) the composition of the bulk mixture, 2) the sequences of the constituent proteins.

 “our findings would provide the field with an understanding of some of the potential pathways utilized by these condensates to control their mutual interactions and their coexistence patterns.”

What are the possible consequences of these findings for your research area?

The assemblies formed by biomolecular condensates play an important role in optimizing their functional output. For example, Brangwynne and co-workers (Feric et al. Cell 2016) have shown that the sub-compartments of the nucleolus are coexisting liquid phases/condensates that show a nested condensate pattern. The layered architecture of the nucleolus (different condensates embedded within one another) is perceived to help in the sequential processing of rRNA in the nucleolus. The different sub-compartments house enzymes that process rRNA transcripts in a stepwise manner, and ultimately the processed rRNA exits the nucleolus to the cytoplasm. It’s intriguing how the different condensates/phases come together to form a three-layered structure that acts as a factory to execute a cellular process. The proximity of the different phases may be crucial for the transport of the products between the phases. Therefore, it is imperative to understand the mechanism which controls such condensate patterns.

In our study, we show that mixture composition and the sequence of the constituent proteins regulate the inter-condensate interaction and their resultant patterns (engulfed, detached or attached). We envision that our findings would provide the field with an understanding of some of the potential pathways utilized by these condensates to control their mutual interactions and their coexistence patterns.

What was the exciting moment (eureka moment) during your research?

Initially, we utilized a recruitment assay as well as Molecular Dynamics (MD) simulations to discover that molecules on the surface of protein-RNA condensates change as we change the composition of the mixture. Since molecules at the surface should predominantly contribute to the inter-condensate interactions, we hypothesized that changing the surface molecules by tweaking the mixture composition should also change the inter-condensate interaction and their coexistence pattern. The most exciting moment for us was when we saw our predicted condensate patterns in our experimental assays. Our hypothesis translated into experimental results, and all pieces of the puzzle came together.

What do you hope to do next?

I want to venture into research concentrated on applications of biomolecular condensates/protein assemblies for drug delivery and vaccine delivery. The biomolecular condensates’ formation, dissolution, patterning as well material properties have been shown to be trigger-dependent (such as temperature, pH, salt, mixture composition, etc.). Due to the ease of formation and modulation, synthetic condensate/membrane-less organelles hold immense promise as drug delivery vehicles.

Where do you seek scientific inspiration?

My major scientific inspiration comes from my PI, my lab members, and my peers. Being constantly surrounded by an ensemble of intelligent, hardworking, and curious people who strive to make progress towards answering significant questions in our field acts as a constant fuel for my scientific quest. Also, as a woman, I am always in awe of the brilliant women scientists doing amazing work in biophysics. Every time I listen about women scientists doing jaw-dropping top-tier research, it inspires me to work harder and add at least a little to the growing knowledge in our field. Researchers like Katalin Karikó are a constant inspiration, whose incessant hard work for years, despite facing all odds, later paved the way for the mRNA covid-19 vaccine.

How do you intend to help Indian science improve?

I firmly believe that science does not have boundaries or international borders. Scientists will always find ways to collaborate beyond borders to achieve excellence. At the same time, I will be indebted to the prolific and competitive scientific environment that nurtured me back home in India. It is still pretty early in my career to pin on how I can contribute and give back to the community. But the area where I can seek to make the maximum contribution at this point is through dedicated work towards my research to contribute to biophysics as an Indian scientist.

Reference

Kaur, T., Raju, M., Alshareedah, I. et al. Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies. Nat Commun 12, 872 (2021). https://doi.org/10.1038/s41467-021-21089-4

Email: tkaur2@bufalo.edu

Dr. Priya Banerjee lab: https://banerjeelab.org/

Edited by: Manveen K. Sethi (Volunteer, Biopatrika)

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