Cracking the Nucleolar Code: MIT Unravels Evolutionary Secrets of the Nucleolus

A single protein can self-assemble to build the scaffold for a biomolecular condensate that makes up a key nucleolar compartment.

Inside all living cells, loosely formed assemblies known as biomolecular condensates perform many critical functions. However, it is not well understood how proteins and other biomolecules come together to form these assemblies within cells.

MITMIT is an acronym for the Massachusetts Institute of Technology. It is a prestigious private research university in Cambridge, Massachusetts that was founded in 1861. It is organized into five Schools: architecture and planning; engineering; humanities, arts, and social sciences; management; and science. MIT's impact includes many scientific breakthroughs and technological advances. Their stated goal is to make a better world through education, research, and innovation.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>MIT biologists have now discovered that a single scaffolding protein is responsible for the formation of one of these condensates, which forms within a cell organelle called the nucleolus. Without this protein, known as TCOF1, this condensate cannot form.

The findings could help to explain a major evolutionary shift, which took place around 300 million years ago, in how the nucleolus is organized. Until that point, the nucleolus, whose role is to help build ribosomes, was divided into two compartments. However, in amniotes (which include reptiles, birds, and mammals), the nucleolus developed a condensate that acts as a third compartment. Biologists do not yet fully understand why this shift happened.

Evolutionary Changes in the Nucleolus

“If you look across the tree of life, the basic structure and function of the ribosome has remained quite static; however, the process of making it keeps evolving. Our hypothesis for why this process keeps evolving is that it might make it easier to assemble ribosomes by compartmentalizing the different biochemical reactions,” says Eliezer Calo, an associate professor of biology at MIT and the senior author of the study.

Now that the researchers know how this condensate, known as the fibrillar center, forms, they may be able to more easily study its function in cells. The findings also offer insight into how other condensates may have originally evolved in cells, the researchers say.

Former MIT graduate students Nima Jaberi-Lashkari PhD ’23 and Byron Lee PhD ’23 are the lead authors of the paper, which was published recently in the journal Cell Reports<em>Cell Reports</em> is a peer-reviewed scientific journal that published research papers that report new biological insight across a broad range of disciplines within the life sciences. Established in 2012, it is the first open access journal published by Cell Press, an imprint of Elsevier.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>Cell Reports. Former MIT research associate Fardin Aryan is also an author of the paper.

Condensate Formation

Many cell functions are carried out by membrane-bound organelles, such as lysosomes and mitochondria, but membraneless condensates also perform critical tasks such as gene regulation and stress response. In some cases, these condensates form when needed and then dissolve when they are finished with their task.

“Almost every cellular process that is essential for the functioning of the cell has been associated somehow with condensate formation and activity,” Calo says. “However, it’s not very well sorted out how these condensates form.”

In a 2022 study, Calo and his colleagues identified a protein region that seemed to be involved in forming condensates. In that study, the researchers used computational methods to identify and compare stretches of proteins known as low-complexity regions (LCRs), from many different speciesA species is a group of living organisms that share a set of common characteristics and are able to breed and produce fertile offspring. The concept of a species is important in biology as it is used to classify and organize the diversity of life. There are different ways to define a species, but the most widely accepted one is the biological species concept, which defines a species as a group of organisms that can interbreed and produce viable offspring in nature. This definition is widely used in evolutionary biology and ecology to identify and classify living organisms.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>species. LCRs are sequences of a single amino acidAny substance that when dissolved in water, gives a pH less than 7.0, or donates a hydrogen ion.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>acid repeated many times, with a few other amino acids<div class="cell text-container large-6 small-order-0 large-order-1">
<div class="text-wrapper"><br />Amino acids are a set of organic compounds used to build proteins. There are about 500 naturally occurring known amino acids, though only 20 appear in the genetic code. Proteins consist of one or more chains of amino acids called polypeptides. The sequence of the amino acid chain causes the polypeptide to fold into a shape that is biologically active. The amino acid sequences of proteins are encoded in the genes. Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food.<br /></div>
</div>” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>amino acids sprinkled in.

That work also revealed that a nucleolar protein known as TCOF1 contains many glutamate-rich LCRs that can help scaffold biomolecular assemblies.

In the new study, the researchers found that whenever TCOF1 is expressed in cells, condensates form. These condensates always include proteins usually found within a particular condensate known as the fibrillar center (FC) of the nucleolus. The FC is known to be involved in the production of ribosomal RNARibonucleic acid (RNA) is a polymeric molecule similar to DNA that is essential in various biological roles in coding, decoding, regulation and expression of genes. Both are nucleic acids, but unlike DNA, RNA is single-stranded. An RNA strand has a backbone made of alternating sugar (ribose) and phosphate groups. Attached to each sugar is one of four bases—adenine (A), uracil (U), cytosine (C), or guanine (G). Different types of RNA exist in the cell: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>RNA, a key component of ribosomes, the cell complex responsible for building all cellular proteins.

However, despite its importance in assembling ribosomes, the fibrillar center appeared only around 300 million years ago; single-celled organisms, invertebratesInvertebrates are animals that do not have a backbone. They make up the majority of the animal kingdom and include animals such as insects, worms, mollusks, and arachnids. Invertebrates are found in almost every habitat on Earth, from the depths of the oceans to the highest mountains. They play important roles in the ecosystem as decomposers, pollinators, and as a food source for other animals. Invertebrates have a wide range of body shapes, sizes, and behaviors, and they have evolved a variety of ways to survive and thrive in their environments.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>invertebrates, and the earliest vertebratesVertebrates are animals that have a backbone and include mammals, birds, reptiles, amphibians, and fish. They have a more advanced nervous system than invertebrates, allowing them greater control over their movements and behaviors, and they are able to move and support their body weight using their spine. Vertebrates are found in many habitats and play important roles in the ecosystem as predators, prey, and scavengers.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>vertebrates (fish) do not have it.

The new study suggests that TCOF1 was essential for this transition from a “bipartite” to “tripartite” nucleolus. The researchers found without TCOF1, cells form only two nucleolar compartments. Furthermore, when the researchers added TCOF1 to zebrafish embryos, which normally have bipartite nucleoli, they could induce the formation of a third compartment.

“More than just creating that condensate, TCOF1 reorganized the nucleolus to acquire tripartite properties, which indicates that whatever chemistry that condensate was bringing to the nucleolus was enough to change the composition of the organelle,” Calo says.

Scaffold Evolution

The researchers also found that the essential region of TCOF1 that helps it form scaffolds is the glutamate-rich low-complexity regions. These LCRs appear to interact with other glutamate-rich regions of neighboring TCOF1 molecules, helping the proteins assemble into a scaffold that can then attract other proteins and biomolecules that help form the fibrillar center.

“What’s really exciting about this work is that it gives us a molecular handle to control a condensate, introduce it into a species that doesn’t have it, and also get rid of it in a species that does have it. That could really help us unlock the structure-to-function relationship and figure out what is the role of the third compartment,” Jaberi-Lashkari says.

Based on the findings of this study, the researchers hypothesize that cellular condensates that emerged earlier in evolutionary history may have originally been scaffolded by a single protein, as TCOF1 scaffolds the fibrillar center, but gradually evolved to become more complex.

“Our hypothesis, which is supported by the data in the paper, is that these condensates might originate from one scaffold protein that behaves as a single component, and over time, they become multicomponent,” Calo says.

Implications for Disease Research

The formation of certain types of biomolecular condensates has also been linked to disorders such as ALS, Huntington’s disease, and cancer.

“In all of these situations, what our work poses is this question of why are these assemblies forming, and what is the scaffold in these assemblies? And if we can better understand that, then I think we have a better handle on how we could treat these diseases,” Lee says.

Reference: “An evolutionarily nascent architecture underlying the formation and emergence of biomolecular condensates” by Nima Jaberi-Lashkari, Byron Lee, Fardin Aryan and Eliezer Calo, 15 August 2023, Cell Reports.
DOI: 10.1016/j.celrep.2023.112955

The research was funded by the National Institutes of HealthThe National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. Founded in 1887, it is a part of the U.S. Department of Health and Human Services. The NIH conducts its own scientific research through its Intramural Research Program (IRP) and provides major biomedical research funding to non-NIH research facilities through its Extramural Research Program. With 27 different institutes and centers under its umbrella, the NIH covers a broad spectrum of health-related research, including specific diseases, population health, clinical research, and fundamental biological processes. Its mission is to seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce illness and disability.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>National Institutes of Health, the National Institute of General Medical Sciences, the Pew Charitable Trusts, and the National Cancer Institute.