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RUFY3: a critical engine component in lysosomal vehicle

Work done in the lab of Dr. Amit Tuli at CSIR-Institute of Microbial Technology (IMTECH), Chandigarh

About author

Gaurav Kumar
Gaurav Kumar

Gaurav Kumar is a CSIR-Senior Research Fellow (PhD student) at the CSIR-Institute of Microbial Technology (IMTECH) in Chandigarh, India, working in the laboratory of Dr. Amit Tuli (Principal Scientist and DBT/Wellcome Trust-India Alliance Fellow). He earned a master’s degree in biotechnology from the All India Institute of Medical Sciences’ (Department of Biotechnology), New Delhi, India. where he worked at the Department of Biophysics under the supervision of Dr. Hariprasad G and used a 2D-DIGE proteomics technique to identify potential protein biomarkers in serum samples from schizophrenia and Parkinson’s disease patients. Gaurav is currently conducting research for his PhD thesis on the molecular mechanisms underlying the positioning and motility of lysosomes in mammalian cells. He employs advanced microscopy and biochemical assays to decipher how lysosome positioning and motility regulate various aspects of lysosome function, a critical organelle involved in cellular homeostasis in addition to serving as the cell’s degradative compartment.

Interview

How would you explain your research outcomes to the non-scientific community?

In terms of functionality, cells, which are the building blocks of our tissues, are quite comparable to a city. In simple words, for a city to operate efficiently, we as people must do our daily tasks, for which mobility and interactions with other individuals is important. Similarly, organelles or compartments in our cells must move and interact with other organelles to execute various essential cellular processes. For instance, proteins that are made in endoplasmic reticulum and Golgi, need to be transported to different cellular locations to execute their function.

Our lab is particularly interested in studying one such organelle, the lysosomes. Because of their well-known involvement in the breakdown of cellular waste, lysosomes have historically been considered as the waste bin of the cells. However, over the last decade, a much more complex scenario of lysosome function has emerged, which has fundamentally changed the perspective of lysosomes. Interestingly, despite being long considered as a garbage bin of the cells, they are now regarded as a controller of various functions, including sensing growth signals and nutrient levels and ultimately deciding the cell metabolism. Lysosomes are shown to be involved in a wide range of cellular and physiological processes, including autophagy, nutrition sensing and signaling, cell membrane repair, immunological response, cancer, and bone degradation.

Lysosome positioning and motility are critical in order for them to fulfill many distinct cellular functions. To comprehend the significance of lysosome positioning and motility, assume there is a fire breakout somewhere, and in order to manage that breakout and rescue people, fire brigades/fighters must hurry to the location. However, if there is a glitch in their vehicle, they will be unable to move or reach the location. Similarly, lysosomes must move and position near the cell membrane in order to conduct functions such as cell membrane repair, antigen presentation, or bone degradation. Furthermore, interruption of lysosome motility has a profound impact on cellular homeostasis. As a consequence, it is not surprising that lysosomal dysfunction is associated with a variety of ailments, including neurological disorders and osteoporosis.

To move from one place to another as per our requirements, we need vehicles, roads, and other accessories. Likewise, for lysosome mobility and function, our cells have molecular motors (vehicles), small G proteins, adaptor proteins (accessories), and microtubule tracks (roads).

Our group is interested in understanding the mechanistic and functions of these molecular machines. Since mechanics can fix vehicles/machines only if they understand how the machines function. Thus, if we wish to cure disorders caused by impaired lysosome motility, we need to understand how these molecular machineries operate.

Model illustrating the opposing motor adaptors recruited by Arl8b. Arl8b binds to SKIP that in turn recruits and activates Kinesin-1 motor to promote anterograde (towards plasma membrane/cell periphery) motility of lysosomes. As revealed in our study, Arl8b recruits RUFY3 on lysosome that in turn interacts with JIP4-dynein-dynactin complex to mediate retrograde (towards nucleus) movement of lysosomes.
Model illustrating the opposing motor adaptors recruited by Arl8b. Arl8b binds to SKIP that in turn recruits and activates Kinesin-1 motor to promote anterograde (towards plasma membrane/cell periphery) motility of lysosomes. As revealed in our study, Arl8b recruits RUFY3 on lysosome that in turn interacts with JIP4-dynein-dynactin complex to mediate retrograde (towards nucleus) movement of lysosomes.

How do these findings contribute to your research area?

Our research has identified a key player RUFY3 in the movement of lysosomes on microtubule tracks. RUFY3 interacts with small G protein Arl8b on lysosomes and the microtubule motor protein dynein. Dynein functions as a vehicle for the lysosomes to move on microtubule tracks. Moreover, Arl8b-RUFY3-dynein mediated lysosome transport also impacts lysosome size, likely by regulating reformation kinetics from these compartments. Thus, our research has revealed the function of a previously uncharacterized protein RUFY3 in lysosome positioning and function. Being a critical mechano-kinetic protein in lysosomal mobility, RUFY3 can potentially offer new perspectives to underlying causes of various lysosomal diseases and pose a potential therapeutic target.

“our research has revealed the function of a previously uncharacterized protein RUFY3 in lysosome positioning and function.”

What was the exciting moment during your research?

Throughout the course of our research, there were several exciting moments. Nevertheless there were two unforgettable instances that I would like to share. First, when I got the Transmission Electron Microscopy (TEM) results, which confirmed our hypothesis regarding the reduction in lysosome size upon RUFY3 depletion. Second, during the review process of our work, a preprint from Prof. Juan Bonifacino’s group (NIH, USA) came out. I was thrilled seeing the similar results and findings in their study (because he is a pioneer in cell biology research). This was an amazing experience for me, as I feel that the reproducibility of findings and outcomes isone of the most fulfilling aspects of this profession.

What do you hope to do next?

When I look at the work of other researchers across the globe, I feel as if I have just recently learned to walk and have a long journey ahead of me. Also, my contribution to science up until now is just a little drop in the ocean. So, my aim is to keep learning and contributing to the advancement of science and society. As previously said, a mechanic can only fix a machine if he or she understands how it works. So, I want to be a skilled researcher (molecular mechanic) so that one day we may exploit molecular machinery of the cells to treat diseases like osteoporosis and neurological ailments. Additionally, I like educating and helping individuals, and in the future, I aspire to assist the less fortunate.

Where do you seek scientific inspiration from?

For me, inspiration does not come from a single source; rather, it comes from every person who gives their all-in whatever they do and are committed to work for the betterment of society. This includes our soldiers, social workers, researchers, and others. I have learnt a lot from individuals around me, and I admire their enthusiasm for science. However, I personally like the kind of work Prof. Manu Prakash’s group (Stanford University, USA) puts out, making him one of my favorites. I hope that one day I will be able to do a little something like him.

How do you intend to help Indian science improve?

There is no question that Indian science has advanced greatly in recent years, but I believe there is still a dearth of a collaborative and multidisciplinary effort. I wish to develop the collaborative work culture among Indian scientists. To put it in another way, we must avoid becoming frogs in wells, working in silos. Moreover, our nation is brimming with talent, but not everyone has access to resources. I wish to assist school students who are really interested in science and want to make an impact on society, but owing to a variety of factors, whether financial or lack of awareness, they are unable to do so.

Reference

Kumar, G., Chawla, P., Dhiman, N. et al. RUFY3 links Arl8b and JIP4-Dynein complex to regulate lysosome size and positioning. Nature Communications 13, 1540 (2022). https://doi.org/10.1038/s41467-022-29077-y

Edited by: Nivedita Kamath

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