New rules for the physical basis of cellular organelle composition

May 06, 2020

New findings about critical cellular structures have upended common assumptions about their formation and composition and provided new insight how molecular machines are built in living cells.

Organelles are the cell's organ-like compartments, which are implicated in many cellular functions including the formation of critical cellular machinery, while also having implications for disease and pathology. A large class of organelles can form without the need for membrane boundaries, and are increasingly referred to as condensates because they are widely believed to form through liquid condensation, like dew drops on grass. But since these organelles have no walls, researchers still do not understand the rules that govern what molecules get into condensates, and what are excluded.

One prediction of the liquid condensation model is that these structures form when the concentration of proteins and other biomolecules becomes high enough to cause them to "condense" from within the surrounding cellular milieu. "It's like adding salt to water. Salt goes into solution; but if you add enough, at some point it stops and salt crystals drop out," said Joshua A. Riback, a postdoctoral researcher in chemical and biological engineering at Princeton University and the article's co-first author, together with former graduate researcher Lian Zhu. "But when we looked at it, we found this is not the case."

The findings, by a researchers at Princeton and the St. Jude Children's Research Hospital in Memphis, were published online May 6 in the journal Nature.

Working with colleagues led by Clifford Brangwynne, a professor of chemical and biological engineering at Princeton and an Investigator at the Howard Hughes Medical Institute, Riback and Zhu found that the formation of the condensates also heavily depended on multiple compounds present in the cell. Researchers previously believed that condensates formed when enough of a single biomolecule, such as protein or RNA accumulated in cells. But the answer is more interesting than that.

"The ratio of different types of biomolecules is very important," Riback said. "It's called compositional dependence."

Or in Brangwynne's analogy: "It's like cooking: did I add too much salt to this recipe? Well, it depends on how many onions are in the pot already!"

One reason for the compositional dependence is the way that proteins and RNA interact at the molecular level. Condensates require a certain amount of interactions, which depends on the types of biomolecules and their compositions. The researchers found that interactions between different types of molecules, or heterotypic interactions, were essential for driving the formation of these structures. Too low or two high of a composition of one biomolecule limits the number of heterotypic interactions which can form.

The researchers demonstrated the importance of this composition dependence for the assembly of critical molecular machines in cells. One example is the creation of the ribosome -- critical for the production of all protein in the cell -- which form in liquid condensates called nucleoli. Riback said the formation of ribosomal subunits is similar to folding origami. When the shape is complete, the ribosomal subunit no longer has enough available regions which can form connections that make it stick to the surrounding liquid within nucleoli. So, it is ejected, allowing it to go out and perform its function throughout the cell.

"As the RNA folds into the origami swan, it can no longer contribute," Riback said. "So if it is properly folded, it is expelled."

Richard Kriwacki, a co-principal researcher for the project, said the findings provide important insight for cellular biology.

"This study highlights how the process of phase separation enables a complex membraneless organelle such as the nucleolus to respond to changing cellular conditions by linking its protein composition to its own functional output, ribosomes, which are the molecular machines that synthesize proteins," said Kriwacki, a member of the St. Jude faculty and co-leader of its Cancer Biology Program. "Our data suggest that, as nucleolar protein synthesis varies in cells, phase separation helps control nucleolar structure, dynamics and function."

The researchers performed the experiments by tagging proteins with fluorescent markers and using the fluorescence to see how varying the protein concentration affected condensates' formation. Riback said the inspiration for the experiment came after they tried to increase the size of condensates by triggering cells to over-express certain types of proteins. When this changed the composition and stability of the condensates, they began to examine the cause.

"I wanted to understand how proteins formed condensates," he said. "It turned out to be a lot more complicated in cells then in the test tube."
Besides Bangwynne, Kriwaki, Riback and Zhu, who is now a senior engineer at Becton Dickinson and Company, the paper's authors include: David W. Sanders and Ming-Tzo Wei of Princeton University; Mylene C. Ferrolino, Michele Tolbert, Diana M. Mitrea of the St. Jude Children's Research Hospital. The research was supported in part by the National Science Foundation, the Howard Hughes Medical Institute, the St. Jude Collaborative on Membraneless Organelles, the Princeton Center for Complex Materials and the National Institutes of Health.

Princeton University, Engineering School

Related Proteins Articles from Brightsurf:

New understanding of how proteins operate
A ground-breaking discovery by Centenary Institute scientists has provided new understanding as to the nature of proteins and how they exist and operate in the human body.

Finding a handle to bag the right proteins
A method that lights up tags attached to selected proteins can help to purify the proteins from a mixed protein pool.

Designing vaccines from artificial proteins
EPFL scientists have developed a new computational approach to create artificial proteins, which showed promising results in vivo as functional vaccines.

New method to monitor Alzheimer's proteins
IBS-CINAP research team has reported a new method to identify the aggregation state of amyloid beta (Aβ) proteins in solution.

Composing new proteins with artificial intelligence
Scientists have long studied how to improve proteins or design new ones.

Hero proteins are here to save other proteins
Researchers at the University of Tokyo have discovered a new group of proteins, remarkable for their unusual shape and abilities to protect against protein clumps associated with neurodegenerative diseases in lab experiments.

Designer proteins
David Baker, Professor of Biochemistry at the University of Washington to speak at the AAAS 2020 session, 'Synthetic Biology: Digital Design of Living Systems.' Prof.

Gone fishin' -- for proteins
Casting lines into human cells to snag proteins, a team of Montreal researchers has solved a 20-year-old mystery of cell biology.

Coupled proteins
Researchers from Heidelberg University and Sendai University in Japan used new biotechnological methods to study how human cells react to and further process external signals.

Understanding the power of honey through its proteins
Honey is a culinary staple that can be found in kitchens around the world.

Read More: Proteins News and Proteins Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to