An interdisciplinary group of scientists has obtained the first detailed
information about the structure of the most destructive group of plant
viruses known: flexible filamentous viruses.
The cost of worldwide crop losses due to plant diseases is estimated at $60
billion annually. Although there are no good estimates of the cost of plant
viruses alone, the viruses are generally considered to be the second
greatest contributor to those losses (after fungi). The 300-plus species of
flexible filamentous viruses are responsible for more than half of all virus
damage.

The findings are published in the October 1 issue of the Journal of Virology
and could lead to new ways to protect crop plants from these viruses. The
structural information that the researchers have obtained may also benefit
researchers interested in using viruses as agents of biotechnology to coax
plants to produce other useful products, such as pharmaceuticals.

?These are very important plant viruses, and we knew almost nothing about
their detailed structure before these studies,? says Gerald Stubbs, the
professor of biological sciences at Vanderbilt University who directed the
study. ?Their flexibility made them very difficult to analyze.?

The project took more than five years to complete and required the combined
skills of scientists from Vanderbilt, the Department of Energy?s Brookhaven
National Laboratory and Argonne National Laboratory, Boston University,
Illinois Institute of Technology and the University of Kentucky using a
combination of complementary imaging techniques. The result of this effort
was determination of the low-resolution structures of two species of
flexible filamentous viruses: soybean mosaic virus and potato virus X.

Amy Kendall, Michele McDonald, Wen Bian, Timothy Bowles, Sarah Baumgarten,
Jian Shi and Phoebe Stewart from Vanderbilt; Esther Bullitt from Boston
University School of Medicine; David Gore and Thomas Irving from Illinois
Institute of Technology; Wendy Havens and Said Ghabrial from the University
of Kentucky and Joseph Wall from Brookhaven National Laboratory all
contributed to the study.

The researchers found that the external protein coats of the two viruses are
extremely similar even though they come from two different viral families,
Potyviridae and Flexiviridae.

?Although the two viruses are unrelated, they have the same outer protein
coat,? says Stubbs. ?Sometime in the past, a member of one family must have
obtained the coat protein gene from a member of the other family, and it
worked so well that pretty soon it was everywhere.?

The exchange of genes between different viruses is a well-known phenomenon
and generally takes place when two viruses invade the same host, Stubbs
says. According to the scientist, this makes it quite likely that a third
family of flexible filamentous viruses, the Closteroviridae, has the same
protein coat as well.

?Actually, the coat protein is not particularly good at protecting the
genome,? says Stubbs. ?It must confer some evolutionary advantage, but we
don?t know what that might be.?

The viruses are much too small to see with an optical microscope. So the
scientists had to use a combination of imaging techniques - cryo-electron
microscopy at Vanderbilt, X-ray diffraction at Argonne and scanning
transmission electron microscopy (STEM) at Brookhaven - in order to identify
the two structures.

?These techniques are very complementary,? says Stubbs. ?People have been
trying to get this structural work started for decades, more than 40 years.
It?s been very difficult and there have been a number of obstacles,
including the fact that it?s very hard to make good samples of these
viruses.?

Even after Stubbs and his colleagues figured out how to make good samples
and analyzed them using X-ray diffraction and traditional electron
microscopy, there were a number of ambiguities in the results. Brookhaven?s
STEM technique provided the definitive answers. Although it could not
determine the structure of the viral protein coat directly, STEM was able to
put boundaries on the number of molecules in each ?turn? of the
spiral-shaped structure, and this allowed the scientists to select the
correct structure from the alternatives they had come up with using the
other techniques.

Some potential applications of these results include engineering molecules
based on the viral structure that interfere with the viruses? ability to
infect plants. Another possibility would be to introduce modified versions
of viruses or to coat protein genes into a plant to protect it from viral
and insect attacks. Yet another possible application would be to use
modified viruses to introduce genes that instruct plants to make other
useful products - for example, antibiotics or other drugs.
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