The concept of central dogma in biology is compellingly simple: even the name suggests a hallowed, unshakeable truth. But in genetics, for each step along the path from gene to protein, scientists have found far more complexity than the simple picture suggests. Now we know that histone modifications, alternative splicing, and RNA interference all regulate how genes are expressed. A study in the Nov. 2 Cell, led by Suzanne Komili in the labs of Pamela Silver and Fritz Roth, suggests a new wrinkle in the genetic fabric: ribosomes, which translate RNA into proteins, may also be more complex than scientists thought. The researchers have found evidence in yeast that the organelles, usually thought to be identical, actually have some specialization.
This new idea arises from investigating yeast’s many duplicated genes that encode ribosomal proteins. These were thought to be redundant, identical twins that perform the same function in cells. But, in fact, the team discovered the proteins have different roles and are not interchangeable. “This is the first demonstration that duplicated ribosomal protein genes are functionally distinct,” said Silver, HMS professor of systems biology. It suggests that ribosomes, depending on which components they carry, may process proteins differently.
This discovery came out of an investigation that seems, at the outset, far removed from the question of ribosome specialization. Komili, a biophysics PhD student, was studying a small but mysterious puzzle related to cell division in budding yeast. In this process, a bud forms from the parent and gradually grows into a daughter cell, while components from the parent are funneled into the emerging daughter. The mother and daughter cells, though not yet separate, develop distinct characteristics. Many of the differences are caused by a protein called Ash1, which is shuttled as messenger RNA to the daughter and translated only at the growing tip of the new cell. Komili was investigating why Loc1, a protein that is strictly confined to the nucleus of the mother cell, is required for safely targeting ASH1 messenger RNA to the bud tip.
“The question was how something in the nucleus affects something at the other end of the cell,” Komili said.
As Komili investigated the problem, she discovered that Loc1’s effect on ASH1’s mRNA might be a direct consequence of its role in assembling ribosomes in the nucleus. In order for ASH1 mRNA to be located properly on the bud tip of the daughter cell, translation must be repressed and then initiated at the bud tip; if either is interrupted, this critical mRNA disperses into the cytoplasm. Perhaps Loc1 is required to assemble ribosomes in such a way that they properly translate ASH1 on the far end of the budding cell.
Another interesting piece of evidence emerged: a screen by another lab revealed that yeast cells lacking Loc1 or any of several ribosomal protein genes had abnormal budding of the daughter cell. Normally, each bud appears next to the site of the previous bud in a specific pattern, but in these knockouts, the budding appeared randomly. “When taken together, these data suggested to me that all of the processes may be linked,” Komili said. Further studies by Komili showed that the same genes that interfered with ASH1’s localization also interfered with this pattern of bud site selection.
What was surprising was that out of this set of 15 genes, 14 had duplicate copies, or paralogs, in the genome. The yeast genome is particularly rich with gene duplications because of a historical event in which the entire genome doubled. Most of the twinned genes were lost over time, but about 10 percent remained. Fritz Roth, HMS associate professor of biological chemistry and molecular pharmacology, said that most people assumed the duplicate ribosomal genes had identical functions but never disappeared because having extras offered some advantage. “It was thought that we have two copies because we need lots of ribosomes,” he explained. In this case, however, one set of these proteins was required for ASH1 localization, while their genetic twins were not. Komili’s work shows for the first time that these paralogs had different functions.
To see if this phenomenon was more widespread, Komili combed through other datasets to look for examples in which removing one ribosomal protein had a different effect than removing its paralog. “When you look at other data, you see a whole host of cases where one paralog shows a different phenotype than another,” Roth said. The team found that the difference in phenotypes was not simply due to one protein being expressed more highly in the cell than another, as had been thought.
Silver explained that the ribosome has a consistent structure based on certain core proteins. But if some of these proteins have different versions with distinct functions, it means that not all of the organelles are the same—they may have specific functions in the cell. The team found that interfering with ribosome assembly had different effects on ribosomes with different paralogs, suggesting they are functionally different.
Silver added that the finding could have implications for other structures in the cell that have duplicate genes. “We have these static structures that people have studied,” she said, “and there could be duplicate genes that have some distinct effects.”
