'Identical' cells? Not so much

Genetically identical cells may be far more different than previously believed. Published this week in linkurl:Science,;https://www.sciencemag.org/ researchers find striking variation in levels of gene expression among individual, genetically identical E. coli, seemingly the result of simple chance. "The paper is quite rich," said linkurl:Sanjay Tyagi,;https://www.phri.org/research/res_pityagi.asp a molecular biologist at New Jersey Medical School who was not involved in the research. "People thi

Written byMegan Scudellari

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Genetically identical cells may be far more different than previously believed. Published this week in linkurl:Science,;https://www.sciencemag.org/ researchers find striking variation in levels of gene expression among individual, genetically identical E. coli, seemingly the result of simple chance. "The paper is quite rich," said linkurl:Sanjay Tyagi,;https://www.phri.org/research/res_pityagi.asp a molecular biologist at New Jersey Medical School who was not involved in the research. "People think that if an organism has a particular genotype, it determines its phenotype -- that there's a one-to-one relationship," said Tyagi. "But as it turns out, [differences in gene expression] can arise just from chance."

Microfluidic device allows multiplex
imaging of library strains.
Image courtesy of Yuichi Taniguchi,
Paul Choi, Gene-wei Li, and Huiyi Chen,
Harvard University

In traditional gene expression studies, researchers grind up a population of cells, then identify overall amounts of gene products from the resulting mixture. Researchers at Harvard University instead studied cells one by one, still calculating averages but also capturing variation in the population with single molecule sensitivity -- and found cells expressing genes at wildly different levels. "It's single molecules meet systems biology," said linkurl:Sunney Xie,;https://bernstein.harvard.edu/pages/AboutProfXie.html senior author on the paper and a chemical biologist at Harvard University. Xie's team, along with collaborators at the University of Toronto in Canada, tagged 1018 genes -- about one-fourth of the E. coli genome -- with fluorescent labels, then counted protein and mRNA copies in individual cells using a high-throughput system. They found that mRNA and protein copy numbers vary greatly from cell to cell, what researchers call "noise." Genes were being expressed at different levels, including some not at all: At any given moment, a fraction of cells didn't have a single molecule of mRNA or protein from a given gene, and a surprising subset of genes -- more than 20 percent of those analyzed -- expressed one or fewer copies of protein per cell. The ability to measure with this kind of single-molecule sensitivity is valuable for single-cell studies, said Xie. "We are able to characterize the protein distribution at every expression level," from single molecules to thousands of proteins, he added. So what causes the variation among genetically identical cells? Chance, researchers said. A single E. coli cell typically contains only a few copies of transcribing complexes at a given moment, resulting in a random synthesis of mRNA and proteins. So whether or not a given gene gets transcribed is a simple numbers game: "It's a mathematical outcome, like throwing a coin," said Tyagi. The researchers also found that, at any moment in time, there is no correlation between a single bacterial cell's protein and mRNA copy numbers, defying the long-held expectation that mRNA levels should correlate with the protein levels in the same cell. Others have showed a similar lack of correlation in populations of yeast. Several factors may be at play, Tyagi writes in an accompanying perspective in Science. First, mRNA have a short lifespan, often only minutes, while proteins are long-lived, sometimes for hours. In addition, because of the short lifespan of an E. coli, dividing every 30 minutes, long-lasting proteins are randomly passed along to daughter cells, so unequal inheritance of proteins may likely lead to some of the noise in bacterial cells. Because mRNA and protein copy numbers don't correlate, scientists need to be careful when attempting to infer protein number from mRNA quantities in a cell. "Single-cell transcriptomes don't tell you what's going on," said Xie. And counting mRNA in a single cell only offers a snapshot, a view of a cell at a moment in time, he added. Scientists can better describe gene expression by examining cells over time. "This is a cautionary note for those who want to do single-cell analysis," said Xie. Y. Taniguchi. "Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells," Science, 329:533-8, 2010.
**__Related stories:__***linkurl:Surpassing the Law of Averages;https://www.the-scientist.com/article/display/55933/
[1st September 2009]*linkurl:Lac on, lac off;https://www.the-scientist.com/article/display/55713/
[1st June 2009]*linkurl:Seeing single protein production;https://www.the-scientist.com/news/display/23231/
[16th March 2006]