A team of researchers headed by biologists at Washington University has sequenced the genome of a unique bacterium that manages two disparate operations — photosynthesis and nitrogen fixation — in one little cell during two distinct cycles daily.
Himadri B. Pakrasi, Ph.D., the George William and Irene Koechig Professor of Biology in Arts & Sciences and professor of energy in the School of Engineering & Applied Science, spearheaded the drive to sequence the genome of Cyanothece 51142, a species that has the ability to produce ethanol and hydrogen. It is the first step in understanding the workings of a bacterium that someday could become an inexpensive renewable energy source.
Cyanobacteria are the only known bacteria to have a circadian clock. By day, cyanothece cells increase gene expression for photosynthesis and sugar production; at night, they moonlight, ramping up gene expression that governs energy metabolism, nitrogen fixation and respiration.
Pakrasi and his collaborators found the presence of a rare linear chromosome in the organism’s genome, a first in cyanobacteria. Further examination revealed the chromosome to be 430 kilobases long and containing a cluster of nine genes that code for enzymes involved in pyruvate metabolism, which is the basis that allows Cyanothece 51142 to produce lactate and other important compounds.
Cyanothece 51142 has one large circular chromosome, the linear chromosome and four small plasmids, which are DNA found outside a chromosome capable of replicating independently.
“This is the first time anything like this has been found in photosynthetic bacteria,” Pakrasi said. “It’s extremely rare for bacteria to have a linear chromosome. Nearly 100 percent of them do not. Now, we have the genome of this organism, which gives us a complete picture of everything that can possibly happen in this cell. The way the cell prospers, multiplies and dies is all decided in the genome.
“This is the benchmark, the prototype, for these cyanobacterial species. Now, we can go back to this complete picture and compare its brother and sister organisms to find their talents and deficiencies. That’s comparative genomics,” Pakrasi said.
Results were published online in the September edition of Proceedings of the National Academy of Sciences.
Washington University collaborating institutions are the Pacific Northwest National Laboratory (PNNL), Saint Louis University School of Medicine and Purdue University. The project was funded by the Danforth Foundation and the National Science Foundation and also is part of an EMSL Scientific Grand Challenge project at the W.R. Wiley Environmental Molecular Science Laboratory, sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research program at PNNL. The majority of the funding came from EMSL.
The researchers found that the majority of proteins on the linear chromosome are hypothetical. But the gene cluster is a major find.
“The linear chromosome contains the only gene copy for lactate dehydrogenase, which facilitates one of the organism’s fermenting capabilities,” said Jana Stockel, Ph.D., a postdoctoral researcher who worked with Pakrasi and fellow postdoctoral researchers Michelle Liberton, Ph.D., and Eric Welsh, Ph.D.
“In conjunction with the proteomics group at Pacific Northwest National Laboratory, we’ve been able to show that many of the genes in the linear chromosome are in fact expressing proteins,” Liberton said. “It’s not just a piece of DNA sitting there. Transcription and translation are happening.”
Comparative genomics is the theme for the next round of Pakrasi’s research. His laboratory has received a grant from the U.S. Department of Energy to sequence the genomes of six other cyanothece organisms in a quest to find the best one to produce hydrogen.
“The goal is to find the hydrogen-producing workhorse of these seven,” Pakrasi said. “Work is ongoing, and I expect in a year or so we will learn a lot more. We will be comparing functions and organizations.”
The strains — two isolated from rice paddies in Taiwan, one from a rice paddy in India and three others from the deep ocean — are related, but each one comes from different environmental backgrounds and might metabolize differently. Thus, one or more strains might have biological gifts to offer that the others don’t, combining traits of the different strains could provide the most efficient form of bioenergy.
Four national laboratories will be involved in various stages of sequencing the other cyanobacteria: PNNL, the Joint Genome Institute (part of Lawrence Livermore Laboratory at the University of California), Oak Ridge Laboratory and Los Alamos Laboratory.
Cyanothece 51142 was sequenced at WUSTL’s Genome Sequencing Center (GSC), based at the School of Medicine. Paper co-author Richard K. Wilson, Ph.D., director of the GSC, and Jeffrey I. Gordon, M.D., the Dr. Robert J Glaser Distinguished University Professor and professor of pathology & immunology, had the original vision to sequence Cyanothece 51142, according to Pakrasi.
“They wanted a pilot program and brought in Danforth Foundation money to get the project going,” Pakrasi said. “Had it not been for their vision and the initial investment, the interest and support from the national laboratories would not be what it is.
“More than four years ago, when we were thinking about cyanothece, we had little idea of the organism’s potential. Today, it’s all blossomed into something much bigger than we’d thought it would,” Pakrasi said.