U.S.-German Research Consortium Sequences Genome of Versatile Soil Microbe

Pseudomonas putida Has Potential for Use in Bioremediation, Promoting Plant Growth and Fighting Plant Diseases

December 2, 2002

In a successful transatlantic collaboration, scientists at The Institute for Genomic Research (TIGR) in Rockville, MD, and at four research centers in Germany have deciphered and analyzed the complete genome of a bacterium, Pseudomonas putida, that has the potential to be used to remediate organic pollutants in soil as well as to help promote plant growth and fight plant diseases.

The genome analysis is published in the journal Environmental Microbiology, which devotes its entire December 2002 issue to articles about P. putida and related Pseudomonas species. The genome paper sheds light on the complex and versatile metabolism that gives P. putida an important role in laboratory research on soil bacteria and also gives the bacterium great potential for bioremediation and other uses.

TIGR's German collaborators in the sequencing project were the Medizinische Hochschule Hannover (MHH) medical college in Hannover; the Gesellschaft fuer Biotechnologische Forschung (GBF) national research center for biotechnology in Braunschweig; the Deutsches Krebsforschungszentrum (DKFZ) cancer research center n Heidelberg; and the sequencing and genomics center of QIAGEN GmbH in Hilden. Professor Burkhard Tuemmler from the MHH was the project's German coordinator. The P. putida project was supported by grants from the U.S. Department of Energy and from the German research ministry, the BMBF.

Associate Investigator Karen E. Nelson, who along with TIGR President Claire M. Fraser led TIGR's component of the sequencing and analysis project, said the availability of the complete genome sequence of P. putida strain KT2440 will make the organism more useful to a range of scientists who are developing new ways to use it and related microbes to clean up organic pollutants.

"This genome provides a great model for microorganisms that have tremendous potential in various areas of biotechnology, such as producing natural compounds, remediating polluted habitats, and fighting plant diseases," Nelson said.

P. putida is a fast-growing bacterium that is found in most temperate soil and water habitats where oxygen is present. Because the bacterium can colonize the root area of crop plants, researchers are trying to use P. putida strains in bioengineering research to develop biopesticides and plant growth promoters. The bacterium is also widely studied because of its diverse metabolism, which is capable of remediating toxic organic pollutants such as aliphatic or aromatic hydrocarbons.

P. putida was designated in 1982 by a National Institutes of Health advisory panel as the first "biosafety" host strain for gene cloning in Gram-negative soil bacteria. The KT2440 strain of P. putida is used by researchers for the analysis and manipulation of genes from soil bacteria.

Kenneth N. Timmis, who led the GBF's component of the project, described P. putida as "a nutritional opportunist par excellence" which plays an important role in maintaining environmental quality in soils and is useful in scientific studies. Timmis said, "Its fascinating biochemistry and physiology, its robustness, rapid growth and ease of handling in the laboratory, and its amenability to genetic analysis and manipulation have resulted in P. putida becoming a laboratory 'workhorse' for research on soil bacteria and bacteria-remediated soil processes."

TIGR, which in 1995 determined the first complete genome sequence of a free-living organism, is a world leader in microbial genomics. The institute has completed the full sequences of 30 organisms or microbial strains, and its scientists are now working on another 75 genome sequencing projects.

The genome analysis found that P. putida has a single circular chromosome with nearly 6.2 million DNA base pairs. An analysis by Nelson and Vitor Martins Dos Santos of the GBF found previously unidentified metabolic pathways in P. putida KT2440 that allow it to transform aromatic compounds, including phenylalkanoates, ferulate, vanillate, and coniferyl- and coumaryl alcohols, aldehydes and acids. TIGR Assistant Investigator Ian Paulsen, who explored the correlation of metabolic pathways with membrane transport capability, said P. putida has "lots of novel pathways and transport capabilities to break down aromatic and other unusual compounds."

The P. putida genome also was compared to that of other species to reveal details about the microbe's evolutionary history. Perhaps the most revealing comparison was with the genome of another member of the Pseudomonas genus - P. aeruginosa, which is an opportunistic pathogen and the leading cause of death for cystic fibrosis patients.

TIGR evolutionary biologist Jonathan Eisen said, "Such comparisons among closely related species with different biological properties are invaluable in learning about the biology of each species. In this case it allows us to better identify the features in the P. aeruginosa genome that contribute to making it a pathogen."

An analysis by Tuemmler and Christian Weinel of the MHH identified numerous chemosensory systems, cell attachment factors, and transport systems in P. putida that had been thought to be involved in virulence in P. aeruginosa. For example the KT2440 (P. putida) genome contains a chromosomal region that is present in 85% of P. aeruginosa clinical isolates from sepsis and urinary tract infections. "That suggests that those genes many not be specific for virulence," said Eisen. The researchers did, however, find many genes in P. aeruginosa and not P. putida that had not previously been identified as candidates for being involved in pathogenicity. The identification of such genes may help biomedical researchers pinpoint potential targets for developing drugs or vaccines against this pathogen.