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Microorganisms have a proven track record for producing powerful molecules
useful in antibiotics, as anticancer agents, and in treating human diseases,
January 2007.

At times, researchers studying the genomes of these microorganisms have
come across sections of DNA for which scientists cannot determine what is
ultimately produced. It's not clear what might be created from these
so-called ?orphan gene clusters? and if those end products might carry
beneficial qualities.

Scientists at Scripps Institution of Oceanography at UC San Diego have
devised a new method for identifying the mysterious products of orphan gene
clusters.

?In this new age of genomics, microorganisms have even more capacity to make
exotic natural product molecules than we ever realized,? said William
Gerwick, a professor in Scripps Oceanography's Center for Marine
Biotechnology and Biomedicine and the Skaggs School of Pharmacy and
Pharmaceutical Sciences at UC San Diego. ?However, sometimes we don't know
how to find these products. We can see them in the genomic information but
we can't necessarily find the resulting organic substances.?

The method developed by Gerwick and his colleagues employs a novel
combination of genomic sequence analysis and isotope labeling. The new
?genomisotopic approach? is described in the new issue of Chemistry &
Biology as the journal's featured cover paper.

Gerwick says the key to the genomisotopic approach lies in the combined
power of bioinformatics-computer programming to predict the proteins as well
as the component building blocks they will use to make the new mystery
product-with the ability to provide building blocks containing distinctive
isotope labels to cultures producing the mystery compound. The microorganism
assimilates the isotope-tagged precursors, incorporates them into the
mystery compound, thus enabling the researchers to ?find? the mystery
compound simply by looking for the isotope signature. According to the
paper, the approach represents a valuable complement to existing genome
?mining? strategies.

?This technique allows us to methodically and with a very well-defined
strategy figure out and isolate the compounds that are produced from those
orphan gene clusters,? said Gerwick. ?With the genomisotopic approach we're
mapping out a metabolic process. We're watching the incorporation of the
amino acid into a more complex natural products structure and visualizing it
at the end by a combination of mass spectrometry and nuclear magnetic
resonance spectroscopy.?

The genomisotopic approach was born out of a failed experiment in Gerwick's
laboratory. A student had attempted to clone the biosynthetic gene cluster
for a certain compound. The student sequenced a stretch of DNA that
initially appeared promising as the correct gene cluster, but ultimately
proved not to be.

?So with that big stretch of DNA we scratched our heads and wondered, if it
didn't make the compound we thought it did, what did it make?? said Gerwick.
?We brainstormed and thought we could come up with an approach for finding
out.?

In addition to describing the genomisotopic approach, the Chemistry &
Biology paper describes the identification of a compound of a previously
unknown natural product discovered through the new method. Gerwick and his
colleagues applied the approach and found what is now known as orfamide A, a
new natural product that may prove beneficial in agriculture and crop
protection due to its potential in suppressing plant diseases.

Gerwick says the new approach will now be applied to various organisms
derived from the ocean, including marine bacteria.

In addition to Gerwick, the paper's coauthors include Harald Gross (Scripps
and Oregon State University), Virginia Stockwell (Oregon State University),
Marcella Henkels (U.S. Department of Agriculture), Brian Nowak-Thompson
(Northland College) and Joyce Loper (U.S. Department of Agriculture).

The study was funded by the National Institutes of Health and the Microbial
Genomic Sequencing Program of the U.S. Department of Agriculture Cooperative
State Research, Education and Extension Service.

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