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Another Minimal Genome: Microbe Needs Just 271 Genes
Edward R. Winstead

A minimal genome is biology’s bottom line. It is the smallest set of genes an organism needs to live in a particular environment. While most microbes have hundreds or thousands of genes, some use only a fraction of these at any one time, depending on their surroundings.

The bacterium Bacillus subtilis needs just 271 genes to live in an experimental environment that is rich in nutrients, a new study has found. The organism has about 4,100 genes.

Stained B. subtilis cells at different stages of sporulation.

“Our study provides the basis for determining how little is needed to make a living cell,” says S. Dusko Ehrlich of Institut National de la Recherche Agronomique in France, who led a team of French and Japanese researchers on the project.

The researchers hope ultimately to construct a minimal genome, using information about different microbes. Hundreds of "essential" genes in bacteria have been identified in recent years, providing a rough idea of what minimal genomes might look like.

The minimal genomes published to date range in number from about 260 genes to 670 genes, depending upon the organism, the environment in which it grows, and the strategy used to calculate which genes are essential.

Interest in minimal genomes is high among scientists because a core set of bacterial genes would be a tool for studying how cells function. It could also be the basis for creating novel microbes that might generate energy or clean the environment, among other things.

To arrive at the number 271, the researchers grew thousands of B. subtilis cells and systematically inactivated one gene per cell. The ideal test of a minimal genome would be to inactivate every non-essential gene in a single cell, but the technology to accomplish this does not yet exist.

“We constructed mutants for all but a very few genes we studied and could thus determine experimentally whether they are essential or not,” says Dusko. Only about six genes could not be inactivated or otherwise silenced.

The vast majority of essential genes in B. subtilis belong to one of five categories, such as “information processing” and “protein synthesis.” Only a few essential genes could not be categorized because so little was known about them.

“One of the interesting aspects of the study was that we found so few essential genes of unknown function,“ says Dusko. “This shows that there are fewer holes in our understanding of the living cell than early studies led us to believe.” Some studies have reported hundreds of essential genes with unknown functions.

Green fluorescent protein (GFP) fused to Mbl protein of B. subtilis. Mbl forms helical filaments, like actin, that are required for defining and maintaining cell shape.

One strategy for defining a minimal genome is to remove or inactivate the entire set of genes thought to be unnecessary until the final genome is complete. Another is to synthesize a minimal genome, then insert it into an environment that allows it to replicate.

The technology for synthesizing relatively short pieces of DNA exists, but not for creating an organism. In July 2002, researchers announced they had synthesized the genome of poliovirus. Viruses do not contain the genetic machinery to replicate on their own, and to synthesize a bacterial genome would be a far more complex task, if it were even possible.

Bacillus subtilis belongs to the family of bacteria that includes the pathogens that cause botulism, pneumonia, and tuberculosis, as well as bacteria used to produce food and industrial products. It was the first gram-positive bacterium to be sequenced.

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Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100, 4678-4683 (April 15, 2003).

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