At this time, most strategies to find out the proteins inside a cell depend on a crude census—scientists often grind a big group of cells up earlier than characterizing their genetic materials. However simply as a inhabitants of 100 single folks differs in some ways from a inhabitants of 20 five-person households, this sort of description fails to seize details about how proteins are interacting and clumping collectively into practical teams.
Now, researchers on the College of Chicago’s Pritzker College of Molecular Engineering (PME) have developed an method that lets them extra simply research whether or not proteins are positioned in shut proximity to one another inside a cell. The know-how, which may be carried out similtaneously extra routine gene sequencing, is described within the journal Nature Strategies.
“It is a streamlined and high-throughput strategy to look into protein capabilities inside particular person cells,” stated Savas Tay, professor of molecular engineering and senior creator of the brand new work. “I believe this methodology goes to be a serious useful resource for the molecular biology group.”
Centered on perform
Lately, with the appearance of quick and low cost genetic sequencing applied sciences, scientists have turned to single-cell mRNA sequencing to get snapshots of cell’s inner states. By sequencing all of a cell’s mRNA molecules—which encode proteins—they will get an thought of what proteins a cell is likely to be actively utilizing. However this sort of proxy for protein abundance would not convey the complete story.
“Simply understanding the abundance of sure proteins would not at all times offer you details about how a cell is functioning,” stated Tay. “Usually, whether or not or not proteins are functionally lively has to do with not simply whether or not they’re current however whether or not they’re forming complexes.”
Tay wished to seize whether or not proteins had been bodily close to one another—and achieve this in a quick, high-throughput means, not by counting on microscopy to visualise their places or isolating a couple of proteins at a time for nearer inspection.
He and his colleagues developed molecular probes that connect to proteins of curiosity and have DNA tags extending outward. If two proteins are bodily shut to one another, these DNA probes stick collectively like Velcro. The researchers can arrange experiments that concurrently probe lots of of proteins on this means. Then, they use routine sequencing strategies to learn again any DNA probes that certain to one another and decide which proteins had been paired up.
“Within the huge area inside a cell, it is not possible for 2 probes to seek out one another except they’re certain to close by proteins,” stated Tay. “So when the probes bind, that tells us these proteins are very shut collectively.”
Because the method, dubbed Prox-seq, makes use of customary sequencing, researchers can analyze a cell’s mRNA similtaneously the proteins of curiosity, to assist reply questions in regards to the correlation between mRNA and protein abundance and performance.
For example the utility of Prox-seq, Tay’s crew first examined it on B cells and T cells, two subsets of human immune cells. The method, they discovered, might differentiate the cells based mostly solely on which protein-protein interactions had been current in every cell sort. It additionally might establish beforehand unknown subsets of the cells based mostly on small variations in how teams of proteins had been organized inside the cells. Utilizing human derived peripheral blood mononuclear cells, they concurrently measured 38 particular person proteins, 741 protein complexes, and hundreds of mRNA on every particular person cell, and found a brand new protein complicated that defines naïve T cells.
Then, the group used Prox-seq to check how proteins change association in macrophages, one other sort of immune cell, when the cells turn out to be activated in response to a pathogen. As soon as once more, they recognized each identified pairs of interacting proteins in addition to new teams of proteins that can be utilized to establish not solely whether or not a macrophage has been activated but in addition what sort of pathogen it was uncovered to.
“This confirmed that not solely can our methodology confirm protein-protein complexes that we already knew about, however it could discover new interactions between proteins,” stated Tay.
Thus far, the researchers have solely examined the strategy on proteins discovered on the floor of cells; they’re now working to increase it to extra kinds of proteins as develop methods to resolve precisely the place inside a cell proteins are interacting.
Luke Vistain et al, Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing, Nature Strategies (2022). DOI: 10.1038/s41592-022-01684-z
College of Chicago
Meet the (protein) neighbors: New methodology lets researchers detect proteins in shut proximity in single cells (2022, December 6)
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