Arlington, Virginia
August 19, 2003

Sequence for model pathogen opens up next level of study for many bacterial diseases

Scientists have sequenced the genome of the microbe that causes bacterial speck disease in
tomato plants and have reported preliminary information about the roles of the more than 5,500 genes, including clues to how the bacterium infects plants that are constantly trying to defend themselves against pathogens. The bacterium's host-infection mechanism is also similar to that used by many other plant, animal and human pathogens, including a number identified as priority targets for the nation's biodefense efforts.

The research team, led by Alan Collmer at Cornell University and C. Robin Buell at The Institute for Genomic Research (TIGR), reports on the sequenced genome of the tomato-infecting strain of Pseudomonas syringae in a paper published online this week in the Proceedings of the National Academy of Sciences. The more than 50 strains of P. syringae infect a wide variety of crops worldwide.

"This model organism will give researchers a leg up on learning about pathogenesis for many other bacteria," said Jane Silverthorne, a program director in the National Science Foundation's (NSF) Plant Genome Research Program, which funded the project. NSF is the independent federal agency that supports fundamental research and education across all fields of science and engineering. "There is a lot to learn from how this bacterium infects tomatoes."

"Pathogenesis is far more complex than anyone had dreamed," said Collmer, a professor of plant pathology at Cornell. "Classical pre-genomic tests [with P. syringae] show only a small set of genes involved in virulence. That's actually not the case. There is tremendous redundancy in the virulence system that we were able to uncover with the genome sequence."

Beyond the sequence of 6.5 million DNA base pairs, made available online in annotated form in April, the team reports in PNAS that the bacterium has nearly 300 genes related to virulence, more than 800 genes of unknown function not found in closely related bacteria, and a large number of so-called "mobile genetic elements." Mobile genetic elements permit the genome to change rapidly and may help P. syringae to interact with plants that evolve new ways to fend off infection.

"This really changes how people approach plant pathology," said Buell, an assistant investigator at TIGR. "People have been doing P. syringae research for years, and the genome sequence has opened up a door to the next level.  You go from trial-and-error exploration to having the whole blueprint in front of you and being able to systematically experiment on specific genetic targets."

While the sequenced strain of P. syringae primarily affects tomatoes, it also infects Arabidopsis thaliana, creating a model pair for plant pathogen studies. In addition, P. syringae is closely related to P. aeruginosa, which can infect humans and animals, and P. putida, a bacterium with uses in environmental cleanup. P. syringae also shares a key infection mechanism with other plant-infecting bacteria that cause diseases ranging from vegetable soft rots to citrus canker. The same mechanism is also found in human-infecting bacteria such as E. coli, Salmonella and Yersinia, the cause of plague-microbes that the U.S. Centers for Disease Control and Prevention have identified as agents
that could pose a risk to national security.

In addition to Cornell and TIGR, the research team includes scientists from the Boyce Thompson Institute for Plant Research, the University of Nebraska, the University of Missouri, Kansas State University and the U.S. Department of Agriculture's Agricultural Research Service (USDA-ARS). The USDA-ARS team, located at the Cornell Theory Center and led by Sam Cartinhour, played a pivotal role in developing computational tools that allowed the researchers to mine the genome for virulence genes.

The team will soon begin working on the genome sequence for a second P. syringae strain. Because TIGR's expertise and facilities for high-throughput sequencing completed the P. syringae project under budget, the team is using the remaining funds to sequence the genome for a strain of P. syringae that infects beans in Africa and other parts of the world. Unlike the tomato variant, however, the bean-infecting strain does not infect Arabidopsis.  Together the two P. syringae strains will provide scientists with valuable comparisons on bacterial virulence and plant resistance.

The bacterial strain described in PNAS is formally known as Pseudomonas syringae pv. tomato DC3000, and the disease it causes, bacterial speck, damages tomato plants in backyard gardens and in crop fields worldwide. The tiny black specks on the plant's leaves and fruits reduce their marketability to grocers, although the tomatoes are still fine to eat. The disease is more prevalent during cool, wet weather, such as the eastern United States has experienced this year. Gardeners can reduce the incidence of the disease by changing the location of tomato plants each season, since the bacteria winter in the soil.

NSF Plant Genome Research Program: http://www.nsf.gov/bio/dbi/dbi_pgr.htm
Pseudomonas Plant Interaction: http://pseudomonas-syringae.org/
TIGR Comprehensive Microbial Resource: http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl

The National Science Foundation (NSF) is an independent federal agency that supports fundamental research and education across all fields of science and engineering, with an annual budget of nearly $5.3 billion. NSF funds reach all 50 states through grants to nearly 2,000 universities and institutions. Each year, NSF receives about 30,000 competitive requests for funding, and makes about 10,000 new funding awards. NSF also awards over $200 million in professional and service contracts yearly.

See also:
Pseudomonas syringae sequenced, providing hope for new defenses in plant and possibly human disease, says Cornell researcher

Abstract and online access to the complete paper: http://www.pnas.org/cgi/content/abstract/1731982100v1?etoc