In microbial genomes, genes are typically depicted as linear series of separate regulatory and coding regions. This leads to the assumption that annotations done by computer to predict such arrangements completely describe the coding capacity of bacterial genomes.
However, the more complex organisms such as plants and animals pack their genes into their DNA very densely. One common packing trick is to code genes on both strands of the DNA, allowing the genes to overlap along the chromosome. Bacterial genes previously shown to reside on the second, or anti-sense, strand overlap just a little -- a couple dozen DNA bases, for example. Less than a handful of genes overlap completely.
To test whether bacteria might be packing genes more tightly than this, scientists at Pacific Northwest National Laboratory and Tufts University compared the proteins made by a bacterial species with what is known about its genome. They chose Pseudomonas fluorescens, Gram-negative rod-shaped bacteria that inhabit soil, plants, and water surfaces.
The researchers analyzed these proteins at the U.S. Department of Energy's EMSL, a national scientific user facility at PNNL, using ultra high-pressure reversed-phase high-performance liquid chromatography coupled to an ion trap mass spectrometer.