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Versatile soil-dwelling microbe is mapped
By Adam Marcus

Scientists have sequenced the genome of one of nature's most versatile microbes, a bacterium called Pseudomonas putida. With an appetite for organic pollutants, the soil microbe has the potential to help clean up the environment. The petroleum industry is investigating P. putida as a cheap means of purifying fuel, while crop scientists are studying its ability to protect plants from pests and help them grow.

A single dividing cell of P. putida.

Researchers have long used P. putida in the laboratory to study the genetics of soil bacteria. In 1982, the US National Institutes of Health designated P. putida a 'safety strain,' meaning it can be used to clone genes from other soil-dwelling germs without fear of contaminating the environment.

The genome sequencing revealed new information about the organism. It has the most genes of any known species involved in breaking down aromatic hydrocarbons, like TNT. Aromatic hydrocarbons are hazardous chemicals generated by the burning of coal, gas, tobacco, meat and other organic matter.

"There are a lot of genes in the genome that we had no idea about before, and we need to go back to the lab and see what this bacterium is really capable of doing," said Karen Nelson, of The Institute for Genomic Research (TIGR) in Rockville, Maryland, who participated in the sequencing project.

The newly sequenced genome may benefit research on cystic fibrosis. Pseudomonas putida is closely related to Pseudomonas aeruginosa (which was sequenced in 2000), the leading infectious killer of persons with this disease. The bacteria have similar genomes, but P. putida lacks certain genes that make its cousin an efficient pathogen, including those for enzymes that digest cell membranes.

The two species have in common 23 of 24 genes known to help the pathogenic strain infiltrate the lungs. The harmless bacterium also has most of the genes that allow P. aeruginosa to evade antibiotics used to kill it.

The pathogen's resistance to antibiotics now seems to be a species-wide trait, says Ian Paulsen, a TIGR scientist who helped sequence both P. putida and P. aeruginosa. These genes, he adds, help P. putida survive antibiotics present in soil, and they may explain its "almost ridiculous" ability to weather environmental toxins, either by breaking them down or pumping them away.

Circular genome map of P. putida. View full

The genome sequence offers bioengineers at least two immediate advances, according to microbiologist Kenneth Timmis, of GBF in Braunschweig, Germany, who collaborated in the mapping of P. putida. The microbe is already considered ‘safe,’ but knowing its genome will allow scientists to ensure it remains benign when foreign genes are introduced. That could aid efforts to exploit its talents in degrading pollutants and fostering crops.

The sequencing revealed at least 80 genes in one family of enzymes, called oxidative reductases, which are involved in breaking down substances in the environment like decomposed connective matter in plants, or lignin.

The bacterium also has hundreds of genes devoted to monitoring chemical signals in its soil surroundings to help it respond to toxins. Unlike certain of its relatives, P. putida appears to lack genes for plant-killing proteins, such as enzymes that break down cell walls, as well as those that cause disease in plants and in people.

P. putida's single ring-shaped chromosome contains roughly 6.2 million base pairs, about two to three times the average for sequenced bacteria. Of those, 5,420 appear to be genes that produce proteins. The findings were published in the journal Environmental Microbiology.

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Nelson, K.E. et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental Microbiology 4, 799-808 (December 2002).

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