Researchers make cell biology quantitative

Yale researchers have reported a method to count the absolute number of individual protein molecules inside a living cell, and to measure accurately where they are located, two basic hurdles for studying biology quantitatively.

Image: Yeast cells with tagged Cdc15p (red) and fimbrin (green) proteins show a contractile ring and actin patches. Credit Jian-Qiu Wu

"The method makes possible accurate measurements of proteins inside cells using microscopic methods usually used just to show where proteins are located," said senior author Thomas D. Pollard, M.D., Chair and Higgins Professor of Molecular, Cellular & Developmental Biology at Yale, of the work published in Science.

Postdoctoral fellow Jian-Qiu Wu attached a tag called yellow fluorescent protein to proteins of interest, allowing these proteins to be detected in live yeast cells with a light microscope. He used seven sample proteins to demonstrate that the brightness of the fluorescence is directly correlated with the amount of that protein in the cell.

With this reference, they could take a stack of pictures through any whole cell that makes a tagged protein, count up all the fluorescent signal, and calculate the number of molecules by comparing with their standardized sample proteins. The assay works whether the molecules are spread out or concentrated in particular parts of the cell, so they could also count the number of molecules in different locations throughout the cell.

Wu assayed the overall and local concentrations of more than two-dozen proteins. Some regulatory proteins had only a few hundred copies, while the common protein actin had millions of copies. The measurements revealed for the first time the ratios of proteins making up structures such as the "contractile ring" that pinches cells apart as they divide.

"People working on yeast should be able to use this method straight out," said Pollard. "Tagging proteins by manipulating their genes is a bit more complicated in other organisms, but it can be done with some work -- even in human or plant cells."

"It is surprising that no one has made this calibration before. Biology has tended to be descriptive," said Pollard. "This technology is part of moving biology to be more quantitative and mechanistic. You can't understand the chemistry and physics of cells without knowing the concentrations of the proteins."

Source: Yale University

Related stories:

Plant steroids offer new paradigm for how hormones work
Steroids bulk up plants just as they do human athletes, but the playbook of molecular signals that tell the genes to boost growth and development in plant cells is far more complicated than in human and animal cells. A new study by plant biologists at the Carnegie Institution used an emerging molecular approach called proteomics to identify key links in the steroid signaling chain. Understanding how these plant hormones activate genes could lead not only to enhanced harvests but also to new insights into how steroids regulate growth in both plant and animal cells.
Prevailing theory of aging challenged in Stanford worm study
Age may not be rust after all. Specific genetic instructions drive aging in worms, report researchers at the Stanford University School of Medicine. Their discovery contradicts the prevailing theory that aging is a buildup of tissue damage akin to rust, and implies science might eventually halt or even reverse the ravages of age.
Adult stem cells activated in mammalian brain
Adult stem cells originate in a different part of the brain than is commonly believed, and with proper stimulation they can produce new brain cells to replace those lost to disease or injury, a study by UC Irvine scientists has shown.
Consortium develops new method enabling routine targeted gene modification
A multi-institutional team led by Massachusetts General Hospital (MGH) investigators has developed a powerful new tool for genomic research and medicine – a robust method for generating synthetic enzymes that can target particular DNA sequences for inactivation or repair. In the July 25 issue of Molecular Cell, the researchers describe an efficient, publicly available method to engineer customized zinc-finger nucleases (ZFNs), which can be used to induce specific genomic modifications in many types of cells.
New study of gene evolution could lead to better understanding of neurodegenerative disease
Genetic evolution is strongly shaped by genes' efforts to prevent or tolerate errors in the production of proteins, scientists at The University of Texas at Austin and Harvard University have found.
A new cellular pathway linked to cancer is identified
In the life of a cell, the response to DNA damage determines whether the cell is fated to pause and repair itself, commit suicide, or grow uncontrollably, a route leading to cancer. In a new study, published in the July 25th issue of Cell, scientists at NYU Langone Medical Center have identified a way that cells respond to DNA damage through a process that targets proteins for disposal. The finding points to a new pathway for the development of cancer and suggests a new way of sensitizing cancer cells to treatment.
Circadian rhythm-metabolism link discovered
UC Irvine researchers have found a molecular link between circadian rhythms – our own body clock – and metabolism. The discovery reveals new possibilities for the treatment of diabetes, obesity and other related diseases.
Novel structure proteins could play a role in apoptosis
Isoforms from Novel Structure Proteins (NSP), a new family of genes discovered by researchers in the Sbarro Institute for Cancer Research and Molecular Medicine in Temple University's College of Science and Technology, could be involved in apoptosis or programmed cell death.

News discussion:

General Science news