As Wood County farmers can tell you, it has been an especially bad year for soybean root rot. Drs. Paul Morris and Vipaporn Phuntumart, BGSU biologists, are part of an international group of 53 scientists working to decode the genomes of the pathogen that causes the destruction, with hopes of derailing it.
Their work is crucial. If left unchecked, the pathogens could destroy not just soybeans but also some of the nation’s most valued forest, and their effects could be felt from coast to coast.
The results of Morris and Phuntumart’s research was reported by lead author Dr. Brett Tyler of the Virginia Bioinformatics Institute in the Sept. 1 edition of the journal Science, describing the genome sequence of two important plant pathogens: Phytophthora sojae and Phytophthora ramorum.
“Phytophtora sojae is a major pathogen of soybeans in the United States, and the economic damage caused by this pathogen was especially evident this year in Wood County,” Morris explained. “While Ohio farmers may not recognize the name Phytophthora (Latin for plant destroyer) they have certainly seen the impact of P. sojae—the causative agent of soybean root rot in their soybean fields.”
Leaf damage on emerging soybeans
Heavy spring rains soon after planting favor spread of the pathogen, resulting in stunting of plants and death of all the plants in low-lying areas.
The economic impact of this pathogen nationwide is estimated to be one to two billion dollars annually. Planting genetically resistant strains is the principle means of minimizing crop losses, but Ohio fields already contain strains of the pathogen that are capable of overwhelming all the soybean cultivars that are presently in use, Morris said.
A national menace
Enter the plant biologists. With the completion of the Human Genome Sequencing project, the major gene-sequencing centers have turned their attention to the genomes of other organisms.
Attacking not only soybeans, Phythophtora species include some of the most destructive plant pathogens, which cause disease in many agricultural crops.
“These organisms have a fungal-like growth habit but are classified in a separate kingdom from fungi,” Morris said. “Certainly the most famous of this group of organisms is Phytophthora infestans, the causative agent of the Irish potato famine of the 1840s and today the most important worldwide pathogen of potatoes.”
Other species in this family are major pathogens of apple and citrus orchards, cocoa, vegetables and forest species. The second strain that was sequenced, P. ramorum, which recently arrived on the West Coast, attacks and kills more than 40 species. (See http://nature.berkeley.edu/comtf/html/p__ramorum_overview.html.)
The impact has been particularly severe on the coastal range ecosystem because the native oak species killed by P. ramorum were the dominant vegetation on those hills. Because this pathogen infects many woody species, including many popular horticultural shrubs, there is concern that it might be accidentally transferred to the East Coast, where its introduction would likely lead to the destruction of oak forests along the Appalachian Range.
When the sequence was first released in June 2004 by the Department of Energy’s Joint Genome Institute, species experts from around the world were invited to an “Annotation Jamboree” in Walnut Creek, Cal., to begin the task of deciphering the unique features of the genome.
“That experience of being in the first group to look at a newly completed genome is easily the most exciting week that I have had as a biologist,” Morris recalled.
Coding for disease-carrying proteins
The BGSU researchers were particularly interested in genes encoding membrane proteins. Membrane proteins are especially important in all plant pathogens because they are likely to be involved in the perception of external signals and in the transport of ions and organic substances across membranes.
During infection, such proteins may be involved in the delivery of toxins to host tissues and in exporting toxins produced by the plant response to infection. This has implications for humans attempting to treat illness, the researchers noted.
Compared to fungal pathogens, the genome of the Phytophthora species contains about 50 percent more genes. This higher number of genes is also reflected in a family of proteins called ABC transporters. In cancer patients, increased ABC transporters results in the failure of chemotherapy because these proteins are capable of pumping numerous drugs out of the cell.
In bacterial and fungal pathogens, an increase in ABC transporters results in resistance to several antibiotics—an emerging and serious problem in hospital settings. The presence of a large number of different proteins of this family suggests that these pathogens are especially well equipped to develop tolerance to plant toxins as well as pesticides applied by humans.
For most protein families, comparison of protein sequences across species and even kingdoms can be used to make predictions of protein function. “That won’t help us to determine the function of almost all of the ABC proteins in Phytophthora species,” Morris said. “ABC proteins have a modular construction of usually four components. From the protein sequence, we can assign all of the proteins to a particular subfamily, and we have some understanding of how they work, but we don’t know what substances they are capable of transporting.
“However, we have already identified a few genes that likely play important roles in the infection process by Phytophthora species in host tissues.”
Adapt or perish
The evolutionary consequence of host-pathogen interactions is that both organisms must continually adapt to changes in defensive or offensive strategies of their opponent, Morris explained. “We are especially intrigued by ABC transporters because some of these proteins play a role in infection by protecting the invading pathogen from plant-synthesized toxins.
“Still other pathogen transporters are likely involved in the delivery of toxins to soybean tissues. We hypothesize that transporters that play decisive roles in the infection process will be undergoing rapid genetic divergence because the plant response has employed counter measures to minimize the effectiveness of these genes.
“The release of two more genome sequences from this family of plant pathogens will enable us to employ large-scale bioinformatic approaches to address these questions. The tools of molecular biology and the wealth of genome data that is accessible via the Internet combine to make this an exciting time to be a biologist.”