How do mRNAs maintain protein levels for long term memory?

Work done in the lab of Prof. Robert Singer at Albert Einstein College of Medicine.

About author

Sulagna Das, Ph.D., is a Research Assistant Professor at Albert Einstein College of Medicine, New York City. Dr. Das completed BSc in Physiology at Presidency College (now Presidency University), Kolkata followed by a Masters in Biotechnology at University of Kolkata. She obtained her PhD in Cellular Molecular Neuroscience at the National Brain Research Center, Gurgaon, under the mentorship of Dr. Anirban Basu. In her PhD work, Dr. Das discovered key mechanisms that cause long term neurological deficits following Japanese Encephalitis Virus infection. Her work led to several publications and received notable media coverage. Dr. Das then moved to the USA for postdoctoral studies pursuing her interests in neuroscience, high-resolution imaging, and RNA biology. Dr. Das has received multiple awards and grants, published several research articles, reviews, and book chapters, and sits on the editorial board of international journals. Dr. Das is a strong advocate for women and minority scientists and is passionate about environmental conservation.

Interview

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

Outcome and Impact of the research:

My research addresses an important question: what goes on in the neuron during the formation of a memory? The brain is made up of billions of neurons connected to each other by bridges called synapses. When we learn, these neurons talk to each other and form new synapses or stabilize the existing ones. As these connections get stronger, our learning or experiences get consolidated and form memories that stay for long. Strengthening the neuronal connections requires new proteins to be made at the synapses and maintained over time. Since proteins are made from messenger RNAs (mRNAs), the neuron performs this precise task of generating “memory-related” proteins by localizing mRNAs to the right place (synapses) and at the right time.

However, the conundrum is: certain mRNAs encoding proteins essential for long term memory are short-lived and disappear within an hour, whereas it takes several hours to form a lasting memory. So, how does this happen? My research addressed this fundamental question, and discovered a potential molecular mechanism underlying memory and paves the way to understand what happens during deficits in retaining long term memory.

How did we do this:

To answer the question defined above, it was important to have the tools to follow the mRNAs and proteins over time in individual neurons. We generated a genetically modified mouse, where we tagged an important memory associated gene called Arc with a fluorescent color so that we could track the entire life cycle of Arc mRNAs – from its production, to where it traveled in the neurons and when it made proteins at the synapses. Using this tool, we discovered a novel phenomenon of gene regulation in neurons: Arc mRNAs produced proteins at “sites” of memory formation, and that led to reactivation of the Arc gene, initiating another round of mRNA synthesis. Strikingly, these new Arc mRNAs recapitulate the original scenario, localize to the same synaptic site, making more new proteins and building up a protein “hub” at the synapses. An interesting feature was how the mRNAs always make their way to the correct location to consolidate the protein pool there. We found that the previous Arc proteins worked as a “cue” or you can think of as a “magnet” trapping the mRNAs from later cycles at that site. Therefore, we identified a novel phenomenon whereby the Arc gene undergoes cycles of gene activation to maintain a hotspot of new proteins over several hours, cementing the synaptic bridges. Think of memorizing a poem- it requires constant repetition to make the memory lasting.

A schematic showing the molecular events in a neuron upon receiving a memory forming stimulus. The dendritic spines are units of synapses (which receive information and are stimulated during learning). Memory forming stimulus activates Arc gene transcription, producing new Arc mRNAs (Step 1) in the nucleus, that travel along the dendrites to reach specific stimulated spines (Step 2). Once they localize, they translate to make new Arc proteins (Step 3) locally, that cluster to form protein “hubs”. Signals from the protein hubs may reinduce a new round of Arc transcription and trap the mRNAs to keep translating more protein to maintain the hub (Step 4). The cycles of new mRNA synthesis and local protein production is a potential mechanism by which neuronal connections are strengthened for long term memory.

How do these findings contribute to your research area?

The findings answered a question that has puzzled scientists for many years- how long-lasting physiological changes for memory can be maintained despite rapid degradation of mRNAs and proteins. These findings have opened up a new avenue of investigating mechanisms by which transient molecular events can be extended into long time scales to impact cellular behavior!

Another important aspect the study revealed, is the power of RNA imaging technology that we developed – in tracking the life of a gene from its birth to its end at the level of a single RNA molecule. We hope that this technique will help researchers answer fundamental questions in gene expression- a critical step for many physiological processes during development and in adulthood.

“The findings answered a question that has puzzled scientists for many years- how long-lasting physiological changes for memory can be maintained despite rapid degradation of mRNAs and proteins.”

What was the exciting moment during your research?

The most exciting moment was to see a single RNA molecule being born and then being transported to the site of memory formation in a nerve cell! The ability to see mRNAs in real time in living cells and brain tissue, performing its function of making proteins when and where the neuron requires them fascinates me every time!

What do you hope to do next?

My research and the findings proposed a new concept in the field of gene expression regulation during memory formation and storage. The next step would be to study what goes wrong in diseases that impact memory – such as in neurodegenerative diseases like Alzheimer’s and in other models of memory loss that happens during aging. I am planning to investigate these questions in my future lab at Emory University School of Medicine, USA.

Where do you seek scientific inspiration from?

I have been lucky to have amazing mentors along my scientific journey. As a kid, I was deeply inspired by my grandfather who was a scientist and a professor, and instilled in me the passion for science and emphasized the power of observation in making scientific discoveries. My PhD advisor, Dr. Anirban Basu (National Brain Research Center, India) dared me to undertake challenging problems even as a graduate student, and my current mentor Dr. Robert Singer (Albert Einstein College of Medicine, USA) keeps motivating me to pursue innovation and out-of-the box thinking in science.

How do you intend to help Indian science improve?

My scientific journey started in India, and I am grateful towards my alma maters – Presidency College, Kolkata and NBRC Gurgaon, for shaping my career. Indian science needs more global exposure and better networking opportunities with international researchers – a goal that I hope to contribute towards. Another important aspect is to promote better outreach opportunities and remove biases in academia. I am part of an organization (BiasWatch India) with a mission towards facilitating a more inclusive scientific community. During the pandemic (2021), we organized an international conference to showcase the research by Indian women scientists and those from minority backgrounds. I would like to continue these efforts supporting young Indian scientists build their career path and promoting science without borders.

Reference

Sulagna Das, Pablo J. Lituma, Pablo E. Castillo, Robert H. Singer. Maintenance of a short-lived protein required for long-term memory involves cycles of transcription and local translation. Neuron 2023. DOI:https://doi.org/10.1016/j.neuron.2023.04.005

Copy Editor

Anjali Mahilkar

Postdoctoral Fellow at University of Michigan

Anjali is an evolutionary biologist working as a postdoctoral researcher in the department of Ecology and Evolutionary Biology at University of Michigan, Ann Arbor. Her research interests mainly lie in understanding the relationship between natural selection, adaptation and drift in deciding the evolutionary fates of biological functions as well as of whole organisms. She has a PhD from IIT Bombay where her research focused on understanding the process of speciation. Anjali also has her Masters from IIT Kanpur and Bachelor’s from NIT Raipur. She also had short work stints at Dr. Reddy’s Institute of Life Science and at a Central University in Chhattisgarh. She is interested in science communication and volunteers for several organizations towards the same. Although not an avid reader, she likes to read fiction in her free time.

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