Finding a Missing Link


Bryant Lab

Bryant&rssquo;s team performed biochemical and genetic analyses on a cyanobacterium called Synechococcus sp. PCC 7002, scouring its genome for genes that might be responsible for making alternative energy-cycle enzymes.

Just because you don’t find it the first time doesn’t mean it isn’t there.

That might be the chief lesson drawn from the recent re-test of a generally accepted 44-year-old theory about how cyanobacteria—the photosynthetic bacteria formerly known as blue-green algae—make energy.

A team of scientists led by Donald Bryant, the Ernest C. Pollard Professor of Biotechnology at Penn State, suspecting that modern genome annotation methods might be perpetuating an old error, decided to try that theory one more time. Their results, published in the journal Science, will require the revision of a lot of textbooks, and may point the way toward new methods for producing biofuels.

As Bryant explains it, back in 1967 two groups of researchers concluded that an important energy-making cycle known as the tricarboxylic acid (TCA) or Krebs cycle (after Nobel laureate Hans Adolf Krebs, who helped discover it), was incomplete in cyanobacteria. The TCA cycle includes a series of chemical reactions that eventually leads to the production of adenosine triphosphate, or ATP—molecules that provide energy for cell metabolism in most forms of life.

The researchers concluded that cyanobacteria were missing an essential enzyme of this metabolic pathway, Bryant explains. “They concluded that cyanobacteria lacked the ability to make one enzyme, called 2-oxoglutarate dehydrogenase, and that this missing enzyme rendered the bacteria unable to produce a compound—called succinyl-coenzyme A—for the next step in the TCA cycle. As it turns out, the researchers just weren't looking hard enough.”

To compound the issue, in today’s genomics, Bryant continues, “Computer algorithms are used to search for strings of genetic code to identify genes. Sometimes important genes simply can be missed because of matching errors, which occur when very similar genes have very different functions. So if researchers don’t use biochemical methods to validate computer-identified gene functions, they run the risk of making premature and often incorrect conclusions about what's there and what’s not there.”

To re-test the 1967 hypothesis, the team performed new biochemical and genetic analyses on a cyanobacterium called Synechococcus sp. PCC 7002, scouring its genome for genes that might be responsible for making alternative energy-cycle enzymes. They found genes that coded for two such enzymes.

“As it turns out, these two enzymes work together to complete the TCA cycle in a slightly different way,” Bryant says, adding that the team went on to find the same genes in all cyanobacterial genomes except those of a few marine species.

In practical terms, Bryant hopes these findings will illuminate new ways of producing biofuels. “Now that we understand better how cyanobacteria make energy, it might be possible to genetically engineer a cyanobacterial strain to synthesize 1,4-butanediol—an organic compound that is the precursor for making not just biofuels but also plastics,” he says.

Bryant also notes that his team’s discoveries show how science is an ever-evolving process, and that firm conclusions should never be drawn from studies with negative results. “In science there is never really an end,” he says. “There always is something new to discover.”

Donald Bryant, Ph.D., is the Ernest C. Pollard Professor of Biotechnology at Penn State and a research professor in biochemistry at Montana State University. He can be reached at dab14@psu.edu.

Last Updated February 22, 2012