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Lean Gene Machine

Ocean bacterium has the most streamlined genome
NO JUNK HERE



DANIELA NICASTRO AND J. RICHARD McINTOSH Boulder Laboratory for 3-D Electron Microscopy of Cells, University of Colorado
Some 25,000 genes code for the proteins required to build each human being, a figure representing only 1 or 2 percent of our entire genome. The remainder is "junk DNA"--base-pair sequences that do not directly code for proteins. But where organisms must operate extremely efficiently to endure hostile habitats, evolution has greatly optimized the DNA, shaving the genome down to what some regard as the minimum genetic requirement to create and develop life.

A new champion in this special bantam-weight class has emerged. An oceanic bacterium, Pelagibacter ubique (or SAR11), one of the smallest self-replicating cells known, has only 1,354 genes, investigators report in the August 19 Science. "SAR11 has almost no wasted DNA," says Stephen J. Giovannoni, the microbiologist who led the collaboration between research groups at Oregon State University and Diversa Corporation (a prospector for useful natural pharmaceuticals and enzymes). Stripped down to the bare essentials for living, the bacterium's gene sequence has almost none of the clutter that most genomes have amassed over time: no duplicate entries, no viral genes, no introns or noncoding sequences. (Many organisms--namely, parasites and symbionts--have smaller genomes, but they rely on others to perform bodily housekeeping tasks.)

Evolutionary biologists believe that the overhead required to maintain junk DNA is justified because it preserves a reservoir of potentially useful genes for a new or changing environment. P. ubique apparently has traded potential for economy in a big way, making its genome the equivalent of a fuel-stingy Volkswagen Beetle, whereas human DNA is more akin to a gas-guzzling Hummer pulling an RV trailer plus a boat.

Paring down the bacterium's genome appears to be evolution's way of conserving genetic energy for an abundant organism in the face of limited resources. First identified in 1990, SAR11 may be the most numerous bacterium on earth (about 1028 cells). It inhabits all oceans and nearly the entire water column. In fact, the tiny bug's combined weight exceeds that of all the fish in all the world's seas.

SAR11 eats dead organic matter that is dissolved in saltwater, what Giovannoni refers to as "a very dilute chicken soup." Because carbon is always available, the minuscule ocean dweller need not develop special biosynthetic pathways and metabolic systems to withstand feast and famine. Indeed, P. ubique's minimal genome is related to its thrifty lifestyle. The shorter the DNA sequence that has to be copied each generation, the less work involved.

The pattern of gene reduction supports the hypothesis that genome streamlining occurs in a very large population for faster or more efficient genome replication, according to Stephen J. Freeland, an evolutionary biologist at the University of Maryland, Baltimore County. "The ability of natural selection to discriminate tiny differences in fitness is affected very much by population size," he explains.

In smaller groups, random genetic drift may determine the fate of genes. With so many copies of the bacterium in the ocean, however, selection can discriminate subtle fitness effects. Essentially, there were so many of the little critters living in a huge, stable environment that they did not go through stress-induced evolutionary bottlenecks during which nonadaptive DNA sequences often get carried along with highly adaptive genes. During the course of a billion years or more, natural selection thus reduced P. ubique's genome size to save on the metabolic burden of replicating DNA with no adaptive value.

"Although natural selection is about the survival of the fittest, what's fittest changes with the specific circumstance," Freeland concludes. The ubiquitous SAR11 embodies just another example of this phenomenon.

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