Researchers Blast Open Pathogen Genome

Image: Courtesy of Tim Elkins BRUTE FORCE: Remnant of an appressorium formed on Mylar. The appressorium produced a peg-like extension that penetrated the film, leaving a round hole. (Reprinted with permission, Annual Review of Microbiology, 50:491-512, 1996.) "The Lord shall smite thee with a consumption, and with a fever, and with an inflammation, and with an extreme burning, and with the sword, and with BLASTING, and with mildew; and they shall pursue thee until thou perish." Deuteronomy 28:22 (Capitalization added) Pity the poor sinner on the receiving end of that damnation. When the scribe invoked blasting, though, he had crop failure in mind rather than explosions. According to the Oxford English Dictionary, a blast in the biblical sense is "a sudden infection destructive to vegetable or animal life," as in "a blasted bud or blossom." Webster's New American Dictionary defines the verb blast as "to damage or destroy by or as by a blight; to wither, shrivel, ruin." Pretty scary imagery, even for today's farmers. But that's just about what happens to rice infected with blast, a disease caused by the fungal pathogen, Magnaporthe grisea. The blight destroys enough rice annually to feed more than 60 million people. "It's the most important pathogen of rice," says University of Georgia mycologist Charles Mims. "Some say it's the most important plant pathogen in the world because of all the people who eat rice," he adds. To make matters worse, Magnaporthe strains infect other grasses including wheat, barley, and pearl millet. The fungus has an even darker side: 'bad guys' could use it as a bioweapon to attack world food supplies, according to the Centers for Disease Control and Prevention.1 Although blast can be controlled with costly and hazardous pesticides, the best strategy is selective breeding for resistant rice cultivars. Unfortunately, "resistance incorporated into rice plants doesn't last very long," according to plant pathologist Barbara Valent of Kansas State University in Manhattan, Kan. Valent, who has worked on rice blast for 20 years, yearns for a more stable resistance regime. Her dream may be a lot closer to reality now that a team of molecular biologists led by Ralph Dean of North Carolina State University in Raleigh and the Whitehead Institute for Biomedical Research in Cambridge, Mass., has completed a draft sequence of Magnaporthe's nuclear genome of 40 million base pairs. The achievement, combined with information from the recently completed rice genome,2,3 could open the way for more effective genetic tools to ward off the disease. According to Patrick Dennis, director of the microbial genetics program at the National Science Foundation, which funded the rice blast project in conjunction with the US Department of Agriculture's microbial sequencing project, "the scientific community needs this information to ... develop new strategies for controlling this destructive pathogen. This will be a springboard for new discoveries." FIRST, SOME BIOLOGY Like a lot of fungi, Magnaporthe has a divided history based on sex. Before they identified its sexual stage, mycologists called the organism Pyricularia rhizae and placed it in an artificial grouping known as the fungi imperfecti. Based on sexual characteristics, they now classify it in the group Ascomycetes, along with Neurospora, Aspergillus, and brewer's yeast (Saccharomyces cerevisiae). Mims and colleagues note that nobody has actually seen Magnaporthe doing sex in nature. So far, the fungus has gone wild only in the lab, enticed by curious researchers. Like other pathogens in the group, blast infects its host in the haploid, asexual state via specialized spores called conidia. When a spore lands on a leaf, it produces special infection structures called a germ tube and appressorium. The latter generates enough penetrating power to pierce Mylar. The fungus has to pass through only the plant's epidermis though to gain access to internal cells, which it kills, thereby freeing vital nutrients. Biologists call that kind of parasite a necrotroph. The resulting streak-like lesions on leaves eventually reduce productivity enough to weaken the entire rice plant. The fungus also invades stems, causing the seed heads, or panicles, to collapse. SEQUENCE, AND BEYOND Principal investigator Dean calls the Magnaporthe sequencing effort "an achievement of huge magnitude." Given the gravitas, one would think it was a long time coming. Dean admits, "It started out slowly, in my lab, but once we got the funds, it took less than a year." Actually, Whitehead spent less than a week assembling the sequence--Magnaporthe's relatively small genome, a tenth the size of rice's blueprint--helped. Image: Courtesy of Tim Elkins DIFFERENT RESPONSES: Magnaporthe grisea germ tubes (Gt), conidium (Co), and appressoria (Ap) react to environmental stresses depend on melanin. (a) The melanized appressorium collapses when placed in high concentration of a nonpermeable solute. (b) After removal of incubation fluid, melanized appressoria remain turgid, while unmelanized structures collapse. (Reprinted with permission, Annual Review of Microbiology 50:491-512, 1996) The next step is to attach meaning to all of Magnaporthe's genes--what molecular biologists call functional genomics. Dean says the group is already hard at work, with the aid of a separate NSF plant genomics grant. "We want the first opportunity to do a global, genomewide analysis," he maintains. That's why the researchers are not immediately releasing the sequence to the GenBank database. Dean and Whitehead will accomodate researchers who want to fish for individual genes, but for now he retains the right to do more comprehensive studies. Dean and fellow blasters will make use of microarrays and directed mutations to probe gene function. Eventually, they hope to generate a complete knockout mutant library of all Magnaporthe genes. "Quite a few researchers will be doing functional genomics" as a result of the sequencing effort, enthuses Valent, who chairs the policy committee that oversees blast genome annotation. Like Dean, Valent wants to decipher how Magnaporthe and its rice host interact during the infection process, which determines disease susceptibility and virulence. Now that both genomes are available, the job will be a lot easier. "We're very much tied to the rice genome" in deciphering plant defense mechanisms, says Dean. "It's very powerful to have both," agrees Valent. With the right gene probes in hand, researchers can get a much better view of the signaling and response steps comprising the dance of recognition between the two species, and hopefully cut in to the benefit of all. The road ahead won't be easy--rice has hundreds of candidate genes involved in disease resistance.3 BROADER IMPLICATIONS Mycologists welcome the Magnaporthe sequence for other reasons too. More than 80 complete bacterial and archaeal genome sequences are on file at GenBank,4 while the Rockville, Md.-based Institute for Genome Research (TIGR) lists 73 on its Web site (www.tigr.org). Many of the archived genomes are from species that infect humans. Other genomes will be completed in the near future. Still, relatively few fungal genomes have been deciphered. "We've had a hard time getting resources," explains Valent. By Dean's count, about a dozen fungal genome sequences reside in private repositories, while half that are available in the public domain, including S. cereviseae and the fission yeast, Schizosaccharomyces pombe. TIGR lists several fungal genome sequences in progress at various sites, including Aspergillus, Pneumocystis, and Candida. Whitehead has the sequence for Neurospora crassa, a workhorse of classical genetics. Neurospora and Magnaporthe are closely related taxonomically. By comparing the two genomes, researchers hope to figure out what makes Neurospora a harmless saprobe and its cousin a lethal pathogen. So far, based on a limited number of short sequences called expressed sequence tags derived from active genes, Dean estimates that the two species are about 60% similar. He expects that number to go up as researchers plumb the full genomes. "I'm really excited about comparing blast with Neurospora," says Valent, who sees even broader implications. "Most fungal pathogens (including Candida, which causes oral thrush in humans) are Ascomycetes, so the blast genome has widespread significance." The Magnaporthe sequence could also provide important evolutionary insights. Louisiana State University mycologist Meredith Blackwell thinks "release of the genome is a boon for evolutionary mycologists who want to discover not only the relationships of fungi, but also the origin and development of traits such as nutritional mode, host relations, and morphology." She adds, "For all its importance as a devastating pathogen, Magnaporthe remains in a poorly sampled lineage." Barry A. Palevitz (palevitz@dogwood.botany.uga.edu) is a contributing editor. References 1. M.G. Kortepeter, G.W. Parker, "Potential biological weapons threats," Emerging Infectious Diseases, 5:523-7, 1999. 2. J. Yu et al., "A draft sequence of the rice genome (Oryza sativa L. ssp. indica)," Science, 296:79-92, April 5, 2002. 3. S.A. Goff et al., "A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)," Science, 296:92-100, April 5, 2002. 4. E. Posey-Marcos, M. Bhagwat, "Searching finished and unfinished microbial genomes," NCBI News, National Center for Biological Information, Spring 2002, p. 6.

Researchers Blast Open Pathogen Genome

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Image: Courtesy of Tim Elkins
BRUTE FORCE: Remnant of an appressorium formed on Mylar. The appressorium produced a peg-like extension that penetrated the film, leaving a round hole. (Reprinted with permission, Annual Review of Microbiology, 50:491-512, 1996.)