Full speed. Half speed. Full stop. Those are the usual choices for controlling the amount of protein produced from a particular gene. Other speeds are possible, but they typically require a lot of effort on the part of scientists, who often resort to the identification and exploitation of a hypomorphic mutation, that is, a mutation that causes a partial loss of gene function. Hypomorphic mutations, however, are usually hard to come by. They may be limited to a specific organism, change gene expression unpredictably, or depend on changes in the spatial–temporal expression of the targeted gene.
Yet problems such as these may be avoided, report scientists based at the Washington University School of Medicine in St. Louis. These scientists assert that they have developed a simple and predictable method to generate hypomorphic mutations in model organisms by targeting translation elongation.
The method appeared January 20 in the journal Nature Communications, in an article entitled, “Rapid Generation of Hypomorphic Mutations.” It can allow scientists to precisely regulate how much protein is produced from a particular gene. The process is simple yet innovative and, so far, works in everything from bacteria to plants to human cells.
“Adding consecutive adenosine nucleotides, so-called polyA tracks, to the gene coding sequence of interest will decrease translation elongation efficiency, and in all tested cell cultures and model organisms, this decreases mRNA stability and protein expression,” wrote the authors of the Nature Communications article. “We show that protein expression is adjustable independent of promoter strength and can be further modulated by changing sequence features of the polyA tracks.”
The polyA tracks, cis-regulatory elements that decrease gene expression by disrupting messenger RNA (mRNA) translation, may be altered by inserting consecutive adenosine nucleotides into the open reading frame of an mRNA. Doing so will decrease protein expression by decreasing the efficiency of translation elongation, the stepwise addition of amino acids to a growing protein chain. Translation elongation takes longer if the progress of the ribosome along the mRNA is slowed.
The molecular machinery that translates the mRNA into proteins has a tendency to stop and slip on a long track of A's before it reaches the end, thereby reducing the amount of protein that is produced.
The Washington University scientists showed that the slipperiness of strings of A's could be used to regulate the amount of protein produced from a gene. The more A's they added to the beginning or middle of a piece of mRNA, the less protein that was produced from it. By carefully controlling the length of the string of A's, or introducing different molecular links in certain position along the string they could produce exactly as much protein as they wanted.
The technique was tested in bacteria, protozoa, yeast, plants, fruit flies, and mouse and human cells. It worked in all of these organisms because RNA translation is an evolutionarily ancient process that occurs the same way across all life forms.
“Basically, this is a universal toolkit for modifying gene expression,” said Sergej Djuranovic, Ph.D., an assistant professor of cell biology and physiology at Washington University School of Medicine in St. Louis, and the study's senior author. “It's a tool that can be used whether you are genetically engineering cells to produce a particular organic molecule, or to study how a gene works.”
The ability to control the amount of protein produced from a particular gene would be a boon to biologists who design or redesign biological systems—such as the set of biochemical reactions that make up cellular metabolism—to produce a desired product. Dr. Djuranovic himself is interested in modulating gene expression to study disease-related genes, such as ones implicated in cancer.
“There are all sorts of complex diseases such as cancer and autism in which we know that expression from a particular gene is dialed down, but nobody knows how that reduction is contributing to the disease,” Dr. Djuranovic explained. “With classical genetics, you can only study what happens when you have two copies, one copy or no copies of a gene, or in other words, 100%, 50%, 0% gene expression. Now we can look at everything in between.”
“The great thing about this is how simple it is,” Dr. Djuranovic concluded. “In the past, if you wanted a mutation that knocked down gene expression by, say, 30%, it took years of work and a lot of luck to find one like that. Now we can do it in a few days.”