Tiny Gene Discovered Hiding in a Major Family of Plant Viruses

AMES, Iowa - In an international collaboration, researchers in Allen Miller's lab in the Department of Plant Pathology at Iowa State University have shown that a tiny gene exists in all members of the largest family of plant viruses. Without this gene, the virus is harmless. The discovery was published recently in the Proceedings of the National Academy of Sciences. The work was based on a prediction made in the lab of John Atkins of University College Cork, in Cork, Ireland. Atkins is a world-renowned expert in the field of "recoding" - genetic decoding events that don't follow the normal rules. A researcher in Atkins' lab, Andrew Firth, turned to computers to discover tiny genes hidden in the sequences of viruses. Firth set his program to work crunching through the genome sequences of the largest and most devastating family of plant viruses - potyviruses. The computer output soon revealed what appeared to be a new gene that overlaps with a much larger and well-known gene in these viruses. At this stage the possible gene was identified simply as a stretch of nucleotide bases in the viral RNA uninterrupted by a "stop" signal and hence known as an open reading frame or ORF. Firth said he thought this was a "pretty interesting potyvirus ORF" so he called it by the acronym pipo and the name stuck. This is where Iowa State entered the picture. Firth and molecular biology graduate student Betty Chung, also of Atkins' lab, temporarily joined the lab of Allen Miller, who is an expert on plant virus recoding, to obtain the necessary materials and expertise needed to investigate plant viruses. This Irish-Iowa State team used a potyvirus called Turnip mosaic virus (TuMV) that had been engineered to express a protein that turns infected plant parts fluorescent green. It was brought to Iowa State previously by Steve Whitham, associate professor of plant pathology. TuMV infects not just turnips, but many important vegetable crops. The researchers altered the sequence of the virus genome so the protein synthesis machinery of the plant cell could not make any protein from the predicted pipo minigene, while all the well-known large genes it overlaps with still could be translated normally. These small mutations "killed" the virus. The normal virus infected plants, causing them to become stunted and glow green under UV light before ultimately dying. The plants inoculated with the mutant virus were healthy and did not glow green because the virus was unable to multiply without the pipo gene. These results indicated this team of scientists discovered a key gene essential to this diverse family of plant pathogens. The mysteries now confronting Miller and Atkins' team are to figure out how the pipo protein is expressed from the viral genome, and what it actually does during virus infection. To answer these questions, Miller and Atkins recently were awarded a nearly $400,000 competitive grant from the USDA National Research Initiative. The team will use these funds to explore what kind of "recoding" event allows translation of the pipo gene, and to determine the process in the virus life cycle in which it is involved. This research is important to agriculture because 30 percent of all plant viruses are in the potyvirus family. These include the potato virus Y, a new strain of which has tormented potato growers in Europe and North America in recent years, Wheat streak mosaic virus which threatens wheat production in Nebraska and elsewhere, and soybean mosaic virus in Iowa which discolors the beans, reducing their market value. Major fruits such as plum and other stone fruits and vegetables such as lettuce and pepper also often are devastated by potyviruses.