A research team from the Virginia Bioinformatics Institute at Virginia
Tech has identified an enormous superfamily of pathogen genes involved in
the infection of plants. The Avh superfamily comprises genes found in the
plant pathogens Phytophthora ramorum and Phytophthora sojae. The pathogen
genes produce effector proteins that manipulate how plant cells work in such
a way as to make the plant hosts more susceptible to infection. The results
suggest that a single gene from a common ancestor of the both pathogen
species has spawned hundreds of very different, fast-evolving genes that
encode for these highly damaging effector proteins.
P. sojae causes severe devastation in soybean crops and results in
$1?2 million in annual losses for commercial farmers in the United States.
P. ramorum, which causes sudden oak death, has attacked and killed tens of
thousands of oak trees in California and Oregon. Both pathogens belong to
the oomycete group of organisms that also includes the potato late blight
pathogen responsible for the Irish potato famine. The scientists probed the
recently published genome sequences of both organisms using bioinformatic
tools that can look for specific amino acid sequences or motifs. Advanced
searches of the genome sequences (BLAST and Hidden Markov Model) revealed
that the P. sojae and P. ramorum genomes encode large numbers of effector
proteins (374 from P. ramorum and 396 from P. sojae) that likely facilitate
the infection of their host plants. Given that there are more than 80
species of Phytophthora pathogens, these findings imply that there are more
than 30 000 members of this superfamily within the genus Phytophthora.

Proteins arising from the Avh superfamily have very different amino
acid sequences but share two common motifs at one end of the protein
(N-terminus). The readily identified RXLR and dEER motifs (single letter
code for amino acids) are required for entry of the proteins into plant host
cells. Similar motifs are also found in the effector proteins produced by
the malarial parasite Plasmodium as it invades red blood cells. The team
also detected some conserved amino acid motifs (W, Y and L) at the other end
(C terminus) of some of the proteins that have been selected over years of
evolution. These C-terminal motifs are usually arranged as a module that can
be repeated up to eight times. The functions of these C-terminal motifs are
being investigated further.

The Avh gene superfamily is one of the most rapidly evolving parts of
the genome. Duplications of genes are common and presumably responsible for
the rapid expansion of the family. The diversity and duplication of genes
noted in the sequences are consistent with maximizing the number of effector
genes in the pathogens while making it increasingly difficult for the host
defense systems to recognize invading molecules, ideal features for effector
proteins aimed at wreaking havoc on susceptible plant hosts. Professor Brett
Tyler of the Virginia Bioinformatics Institute, the leader of the project,
remarked: ?The extraordinary speed with which the Avh genes are evolving
suggests that these genes are key to the pathogens? ability to outwit the
defense systems of the plants.?

The research appears in the March 25 issue of The Proceedings of the
National Academy of Sciences (vol. 105, no. 12, pp. 4874-4879, 2008) in the
article "RXLR effector reservoir in two Phytophthora species is dominated by
a single rapidly evolving superfamily with more than 700 members.? The
research was supported by funding from the National Research Initiative of
the United States Department of Agriculture Cooperative State Research,
Education and Extension Service, from the United States National Science
Foundation, and the Netherlands Genomics Initiative.

The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a
research platform centered on understanding the ?disease triangle? of
host-pathogen-environment interactions in plants, humans and other animals.
By successfully channeling innovation into transdisciplinary approaches that
combine information technology and biology, researchers at VBI are
addressing some of today?s key challenges in the biomedical, environmental
and plant sciences.


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