Huge virulence gene superfamily responsible for devastating plant diseases

April 02, 2008

Blacksburg, Va. - 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."
-end-
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.

Virginia Tech

Related Genome Articles from Brightsurf:

Genome evolution goes digital
Dr. Alan Herbert from InsideOutBio describes ground-breaking research in a paper published online by Royal Society Open Science.

Breakthrough in genome visualization
Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome.

Sturgeon genome sequenced
Sturgeons lived on earth already 300 million years ago and yet their external appearance seems to have undergone very little change.

A sea monster's genome
The giant squid is an elusive giant, but its secrets are about to be revealed.

Deciphering the walnut genome
New research could provide a major boost to the state's growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California's 4,800 growers.

Illuminating the genome
Development of a new molecular visualisation method, RNA-guided endonuclease -- in situ labelling (RGEN-ISL) for the CRISPR/Cas9-mediated labelling of genomic sequences in nuclei and chromosomes.

A genome under influence
References form the basis of our comprehension of the world: they enable us to measure the height of our children or the efficiency of a drug.

How a virus destabilizes the genome
New insights into how Kaposi's sarcoma-associated herpesvirus (KSHV) induces genome instability and promotes cell proliferation could lead to the development of novel antiviral therapies for KSHV-associated cancers, according to a study published Sept.

Better genome editing
Reich Group researchers develop a more efficient and precise method of in-cell genome editing.

Unlocking the genome
A team led by Prof. Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells.

Read More: Genome News and Genome Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.