How Many Proteins in a Cell? Study Answers a Fundamental Question

Proteins are the material that make up our cells and undertake most of the work that goes on in them. Despite the vast volume of research into the function and form of proteins, no study has ever been able to calculate the number of proteins contained within a cell. A new study, led by Grant Brown, a biochemistry professor in the University of Toronto's Donnelly Centre for Cellular and Biomolecular Research, has changed that. Interrogating data from almost two dozen studies of the protein content of yeast cells, the team was able to estimate a reliable number of molecules for each protein in the cell for the first time, reaching a figure of 42 million total protein molecules per cell. 

The work, published this week in the journal Cell Systems, was done in collaboration with Anastasia Baryshnikova, Principal Investigator at Calico, a California biotechnology company that focuses on aging.

Explaining the work, Brown said "The cell is the functional unit of biology, it's just a natural curiosity to want to know what's in there and how much of each kind."

Having a tally of cellular proteins is useful for more than just satisfying curiosity. Many diseases are caused by unusual variation in protein number, and improved knowledge about protein abundance and its regulation could lead to treatments and therapies for these diseases.

Previous studies looking at protein number reported findings in arbitrary units, sowing confusion in the field and making comparison between labs extremely difficult.

Many groups, for example, use fluorescent tags attached to protein molecules to measure abundance, inferring their abundance from how much the cells glow. But differences in instrumentation mean different labs often record completely different levels of brightness emitted by the cells. Other labs measure protein levels using completely different approaches.

"It was hard to conceptualize how many proteins there are in the cell because the data was reported on drastically different scales," said Brandon Ho, graduate student in the Brown lab who did most of the work on the project.

To solve the problem of arbitrary unit use, Ho turned to baker's yeast, a  single-cell microbe that offers insight into basic cell function. Yeasts are also extremely widely studied, enabling calculation of molecule number for each of the 6,000 proteins encoded by the yeast genome. Ho made use of 21 separate studies that measured abundance of all yeast proteins. No such datasets exist for human cells where each cell type contains only a subset of proteins encoded by the 20,000 human genes.

This vast data supply enabled Ho to summarise the field’s findings, benchmark them and convert the vague, uninformative measures of protein number into "something that makes sense, in other words, molecules per cell," said Brown.

Ho's analysis reveals for the first time how many molecules of each protein there are in the cell, with a total number of molecules estimated to be around 42 million. Most of the proteins assessed exist within a narrow range of between 1000 and 10,000 molecules. Some are bountifully present at more than half a million copies, while others are sparsely seen, totalling just 10 molecules per cell.

Interpreting the data, researchers focussed on the mechanisms by which cells control abundance of distinct proteins, enabling similar study using human cells that could help reveal molecular roots of disease. They showed that a protein's supply correlates with its role in the cell, which means that it may be possible to use the abundance data to predict what proteins are doing.

Finally, in an experiment that assuages a long-held fear in modern cell biology, Ho showed that the common practice of adding fluorescent tags onto proteins has little effect on their abundance. While the approach has revolutionized the study of protein biology, netting its discoverers Osamu Shimomura, Martin Chalfie and Roger Tsien the Nobel prize in chemistry in 2008, it also fuelled worries that tagging could affect protein durability, undermining the data.

"This study will be of great value to the entire yeast community and beyond," said Robert Nash, senior biocurator of the Saccharomyces Genome Database that will release the data to researchers worldwide. He also added that by presenting protein abundance "in a common and intuitive format, the Brown lab has provided other researchers with the opportunity to reexamine this data and thereby facilitate study-to-study comparisons and hypothesis generation."

This article is based on work conducted at the University of Toronto.