Scientists trying to grasp the physical and chemical properties that govern biomolecular condensates now have a vital method to measure pH and other emergent properties of those enigmatic, albeit necessary cellular compartments.
Condensates are communities of proteins and nucleic acids. They lack a membrane and are available together and disintegrate as needed. The nucleolus is a distinguished condensate in cells. It serves vital roles in cellular physiology and is the location of ribosome production.
Ribosomes are the multi-protein and RNA assemblies where the genetic code is translated to synthesize proteins. Impairment of ribosome production and other nucleolar dysfunctions lie at the center of cancers, neurodegeneration and developmental disorders.
In a primary for the condensate field, researchers from the lab of Rohit Pappu, the Gene K. Beare Distinguished Professor of biomedical engineering, and colleagues within the Center for Biomolecular Condensates within the McKelvey School of Engineering at Washington University in St. Louis, found out how nucleolar sub-structures are assembled. This organization gives rise to unique pH profiles inside nucleoli, which they measured and compared with the pH of nearby non-nucleolar condensates including nuclear speckles and Cajal bodies.
Within the study, published online in Cell, the authors report that the distinct protein compositions of nucleoli give them an acidic character, whereas nuclear speckles have the identical pH because the nucleus, and Cajal bodies are more basic.
Constructing on spatial proteomics data from the lab of Emma Lundberg, associate professor of bioengineering at Stanford University, and novel algorithms developed by Kiersten Ruff, a staff research scientist at McKelvey, and colleagues within the Pappu lab, the team identified unique “molecular grammars” including the presence of proteins with long acidic tracts as a key defining feature of many nucleolar proteins. This, the team reasoned, must help carry hydrogen protons into nucleoli (pH is the measurement of the activity of protons).
Condensates are like a gathering of individuals on a convention floor. There are not any partitions keeping them in place; just sparkling conversations led by a number of key individuals — the “scaffolds.” The community of molecules that come together enables emergent properties within the condensates, like internal pH in nucleoli.
Condensates form via a process that the team now refers to as condensation. This combines phase separation — think demixing of oil and water — and sticky interactions amongst molecules that wish to bind with each other.
“Biomolecules are defined by a mix of specific interactions and distinct solubility profiles. Condensation involves the totality of those interactions, and this provides rise to what are generally known as emergent properties,” said Matthew King, postdoctoral fellow within the Pappu lab and lead creator of the paper.
The brand new research provides a place to begin for understanding how emergent properties, whereby the entire is bigger than the sum of its parts, give rise to condensate-specific “physicochemical barcodes,” in keeping with King.
Differentials in pH between condensates and the encompassing nucleoplasm generate gradients and “a pH gradient generates what’s generally known as a proton driver,” King said.
This proton driver, measured to be -88 mJ per proton, “might give you the chance to facilitate directional movement of RNA and protein molecules, which is a key first step in enabling ribosomal assembly,” King added.
Getting chemical probes to the best place in cells and to measure the condensates required technological innovations that included contributions from McKelvey project partners Michael Vahey assistant professor of biomedical engineering, and Matthew Lew, associate professor of electrical and systems engineering.
Based on Pappu, this work “provides a chic solution to the challenge that many biochemists see for the condensate concept.”
Cellular reactions require specificity. Every biochemical response must happen in the best place, at the best time, and must involve specific sets of proteins and nucleic acids.
“Condensates were often criticized as being non-specific blobs,” Pappu said.
Because of this latest research, those blobs clearly have specific physiochemical properties.
“We now have evidence that distinct compositional biases of condensates generate distinct physicochemical environments, and this might provide the premise for biochemical specificity,” Pappu noted.
