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Tiny Worlds, Big Science: MDIBL Scientists See Deeper Inside the Cell

  • November 16, 2022

Sometimes a new tool can spur a scientist to unexpected discoveries. 

MDI Biological Laboratory’s Emily Spaulding, Ph. D., is using advanced “super-resolution” microscopy to peer deep within the active cells of a tiny, transparent roundworm called C. elegans.

What she’s found there is a powerful new tool for studying the functions of a common gene protein called Nucleolin. And the work offers a challenge to some recent theories about the gene’s role in human diseases. 

C. elegans’ transparency allows us to do super-resolution imaging, so we can see cellular substructures and processes that are associated with neurodegenerative diseases such as Alzheimer’s and ALS,” Spaulding says. “Very little of this kind of work has been done in a living animal, almost none.”

Spaulding is a post-doctoral fellow in the lab of MDIBL Associate Professor Dustin Updike, Ph.D. This month they published their findings in the peer-reviewed science journal, Nature Communications.

worms under a microscope C. elegans. Photo: Updike lab

During the research, they discovered a new, human-like gene in C. elegans. They dubbed the gene “NUCL-1”, an indicator that it provides a research model for Nucleolin, which in humans is linked to neurodegenerative disease and cancer.

“Nucleolin is a multifunctional protein conserved across many animals, plants, and fungi, but previously thought to be absent in nematodes,” Spaulding says. “It’s also associated with familial ALS and Alzheimer’s disease, and overall nucleolar dysfunction is linked to neurodegeneration.”

Nucleolin is found mainly in the nucleolus, the factory inside a cell’s nucleus where ribosomes are assembled. Unlike many other “organelles” that are bound by membranes within a cell, the nucleolus behaves like a large liquid droplet, also called a condensate.

Condensates form through what’s called “liquid-liquid phase separation”, a process that’s been the subject of intense research – and some debate – over the last decade. Some scientists compare it to blobs of different densities forming inside a lava lamp, but exactly how it works in living cells is still unclear.

Spaulding and Updike’s work shows that NUCL-1 is an essential contributor to phase separation in the C. elegans nucleolus.

Surprisingly, disrupting phase separation in the germline had no effect on health or fertility

Super-resolution image of a nucleolus in a live, wild-type C. elegans nematode, left, shows well-organized architecture of interior condensates. At right, when a newly discovered coding gene called NUCL-1 is disrupted in a mutant worm, the architecture falls apart. Contrary to some thinking about the function of nucleolus substructures, both wild-type and mutant worms were healthy, developed normally, and retained fertility. (Photo: Emily Spaulding, Ph.D.)

Spaulding likens the nucleolus to a Tootsie Pop. “It’s got layers from the inside out,” she says. “Some proteins are localized to the innermost layer, and some proteins localize to the outermost layer. And each of these layers is thought to represent a step in ribosome biogenesis.”

The biological significance of condensate substructure is still under question; recent arguments hold that the precise, tiered spatial organization of the nucleolus – its Tootsie Pop architecture — is essential to ribosome production and the nucleolus’ functionality.

But the MDIBL scientists observed that while removing a key protein domain of NUCL-1 in transgenic C. elegans disrupted the subcellular architecture of reproductive cells (see illustration above), the mutant worms still developed normally and produced normal offspring.

“We noticed that the nucleolus lost its beautiful substructure when we took away the domain, but the worms were totally fine” Spaulding says. “That was a surprise.”

“It’s hinting that maybe this precise organization into layers isn’t as important as we thought to nucleolar function,” she adds. “And this could be important for understanding ALS or Alzheimer’s Disease, where widespread disrupted phase separation is thought to contribute to disease.”

“It will be something that really impacts the field of phase separation, because a lot of the conclusions being drawn may be incorrect,” says Updike. “The results should be of widespread interest and will spark new avenues of study in the fields of phase separation, nucleolar structure and function, and Nucleolin-associated human disease.”

Spaulding is a 2022 recipient of the National Institutes of Health’s Outstanding Scholars in Neuroscience Award.

Link to the Nature Communications article, “RG/RGG repeats in the C. elegans homologs of Nucleolin and GAR1 contribute to sub-nucleolar phase separation”: https://doi.org/10.1038/s41467-022-34225-5


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