Tools from the human genome project reveal a versatile microbe

Now that the human genome has been sequenced, sequencing know-how is turning to other organisms. A team of researchers, including some from the University of Iowa, has sequenced the genome of a highly versatile and potentially useful bacterium. The multidisciplinary effort determined the complete genetic sequence of Rhodopseudomonas palustris, a bacterium that could potentially be used for cleaning up toxic industrial waste and as a biocatalyst for producing hydrogen as a bio-fuel.

The research, conducted by scientists in the UI Roy J. and Lucille A. Carver College of Medicine together with colleagues from Ohio State University (OSU), the University of British Columbia and the United States Department of Energy’s (DOE) Joint Genome Institute, appeared in Nature Biotechnology advance online publication on Dec. 14.

Caroline Harwood, Ph.D., UI professor of microbiology and senior author of the study, explained that the opportunity to investigate this bacterium’s genes arose from DOE interest in sequencing microbial genomes. These organisms have capabilities that could be useful in tackling environmental issues such as energy production, global warming and bioremediation of toxic waste.

In 1997 the DOE established the Joint Genome Institute (JGI) to help sequence the human genome. With the completion of the human genome, the DOE has turned the JGI’s considerable sequencing know-how to other projects, one of which is sequencing microbial genomes.

Rhodopseudomonas palustris (R. palustris) was chosen for sequencing for a number of reasons. It is very good at producing hydrogen, which could be useful as a bio-fuel, and it can degrade chlorine- and benzene-containing compounds that are often found in industrial waste. It also can remove carbon dioxide, a gas associated with global warming, from the atmosphere.

Scientists at Lawrence Livermore National Laboratory used high-tech sequencing machines to sequence the genome and sophisticated software to piece the genome together. Scientists at Oak Ridge National Laboratory, led by Frank Larimer, Ph.D., then performed computational analysis of the entire genome, identifying 4,836 potential genes and assigning likely functions to those genes.

Once this computational effort was completed, every gene had to be “checked by hand” to confirm the computational assignments. To accomplish this task, Harwood assembled a group including scientists from her UI lab who study nitrogen fixing genes, OSU scientists who work on carbon dioxide fixation, and scientists from the University of British Columbia who study photosynthesis.

“We divided up the genes based on specialization area, and each person had to check about 800 genes,” Harwood said.

Most living organisms are capable of using only one of four metabolic modes to live. Humans, for example, obtain carbon and produce energy by consuming organic material, while green plants obtain carbon from carbon dioxide and produce energy from light. In contrast, R. palustris has the genetic capability to use all four metabolic modes depending on the conditions of its immediate environment.

“Once we saw the sequence, we realized what tremendous metabolic versatility this bacterium has,” Harwood said.

Further examination of the genome sequence revealed even greater metabolic versatility and suggested expanded utility for this organism in biotechnology.

The researchers found that even within given metabolic modes, this bacterium has options. For example, most bacteria have one light-harvesting protein that is arrayed like an antenna on the cell surface. The genome sequence suggests that R. palustris actually has five different kinds of light harvesting protein and that it mixes and matches them to get the maximum energy from the available light.

This bacterium’s metabolic range also is seen in the nitrogenase enzymes it uses to fix nitrogen — a process that converts atmospheric nitrogen into ammonia. Only bacteria can fix nitrogen, and the process is very important in agriculture as it replenishes the soil’s ammonia, which improves fertility. A by-product of nitrogen fixation is hydrogen, which can be used as fuel.

Almost every bacterium that fixes nitrogen has just one nitrogenase enzyme. So, the researchers were surprised to find that R. palustris had genes not only for the standard nitrogenase, but also for two additional nitrogenase enzymes. The presence of these additional nitrogenases probably contributes to the ability of R. palustris to make large amounts of hydrogen.

“From an agriculture point of view, the production of hydrogen has been viewed as a bad thing, because the bacteria waste a great deal of energy producing hydrogen that they could be using to feed ammonia to the plant,” Harwood said. “However, if you are interested in making hydrogen as a bio-fuel, this bacterium is extraordinarily good at making large amounts of hydrogen and it has the ability to get the energy to do this from light.”

Although this bacterium is not currently used in an industrial setting as a biocatalyst to produce hydrogen, several labs in Europe and the U.S. are exploring this possibility.

“What makes this bacterium particularly good as a biocatalyst is that it is never energy-limited as long as you can shine enough light on it,” Harwood said. “The process of hydrogen production requires a great deal of energy, so regular bacteria would have to feed on glucose to make that energy, but R. palustris doesn’t have that constraint.”

In addition to Harwood, the UI researchers involved in the study included Janelle Torres y Torres, Ph.D., Caroline Peres, Ph.D., Faith Harrison and Jane Gibson, Ph.D.

The Biological and Environmental Research program of the DOE Office of Science and Technology funded the study.

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STORY SOURCE: University of Iowa Health Science Relations, 5135 Westlawn, Iowa City, Iowa 52242-1178