GM and fungus- Researchers Blast Open Pathogen Genome

[Guest guest]

(( and the point that their are thousands of people in labs all over the

world messing with genetics and doing mutating studies, so where do all the

remnants of their experiments go, and lots are field tested directly in the

environment)))

Researchers Blast Open Pathogen Genome

Results have direct impact on fungal disease of rice | By Barry A. Palevitz

http://www.the-scientist.com/yr2002/aug/palevitz_p24_020819.html

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 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 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. ( 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@...) is a contributing editor.

References

1. M.G. Kortepeter, G.W. , " 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. ©2002, The Scientist Inc.