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Tiny gene discovered in largest family of plant viruses

Iowa State University researchers have discovered that a tiny gene exists in all members of the largest family of plant viruses, without this gene, the virus is harmless.

May 29, 2008  By Iowa State University

27, 2008

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

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

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


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