Gene Clusters Offer Potential Protection Against Plant Diseases

Within every genome, there are chunks of DNA whose functions are unknown. Some of these are similar to genes that make natural products. Because scientists don't know which specific natural products these genes make, these segments are known as "orphan gene clusters."

According to Joyce Loper, a plant pathologist at the ARS Horticultural Crops Research Laboratory in Corvallis, Ore., it's likely that some orphan gene clusters produce natural products that could become new antibiotics. Identifying these gene clusters and their products would give scientists new tools that can be used to fight harmful microorganisms.

Working with scientists at Scripps Institution of Oceanography at University of California-San Diego, Oregon State University, and Northland College in Ashland, Wis., Loper investigated a new method for determining the products of orphan gene clusters.

The scientists used what they call a "genomisotopic" approach, which combines genomic sequence analysis and isotope-guided fractionation, the process of isolating compounds.

Loper and her colleagues applied the genomisotopic method to the genome of the bacterium Pseudomonas fluorescens Pf-5, a biological control agent that protects plants from diseases. Scientists have long known that Pf-5 makes antibiotics, but by using the method, they've identified two antibiotics that had never been seen before.

These studies were funded jointly by ARS, the National Institutes of Health, the German Research Foundation, and the Microbial Genomic Sequencing Program, an initiative of the USDA Cooperative State Research, Education and Extension Service (CSREES). In 2007, CSREES funded the sequencing of seven additional Pseudomonas species, four of which are under investigation in ARS laboratories.

Further research could identify new natural products with valuable properties, with potential for use in antibiotics, drugs or pesticides.