Scripps Team Part of Collaboration that Reveals First Ecological Genomic 'Blueprints'

A broad international collaboration of scientists has uncovered the first genetic blueprints of organisms critically important in the world's ecological makeup.

The genetic blueprints, or genomes, are publicized jointly in the August 13, 2003, online editions of the journals Nature and the Proceedings of the National Academy of Sciences. A group from Scripps Institution of Oceanography at the University of California, San Diego, led one of the discoveries.

The papers describe the genomes of Synechococcus and Prochlorococcus, tiny organisms that account for up to two-thirds of the carbon dioxide "fixation" (the conversion of carbon dioxide into organic compounds during photosynthesis) in the oceans and are key players in marine food webs. By knowing their genetic makeup, the scientists say, researchers will better be able to understand how these organisms process carbon, leading to a better understanding of the global carbon cycle.

"Having these genomes is helping us understand ecosystems in a way no other genomes have before," said Brian Palenik, lead author of one of the Nature papers and a member of the new Center for Marine Genomics at Scripps Institution. "Many of the sequenced genomes to date have been pathogens, but these are the first genomes of organisms that are ecologically relevant on a global scale. So these are really going to help us understand global carbon fixation and global element cycling-these are keystone organisms in marine ecosystems."

The Center for Marine Genomics at Scripps is a new center that will examine the genomes of diverse marine organisms to understand their adaptations to the marine environment.

Synechococcus and Prochlorococcus, single-celled organisms about 1/100th the diameter of a human hair, numerically dominate the phytoplankton of the oceans. With the genomes in hand, researchers will have a better idea of how to solve mysteries surrounding these organisms, such as how they thrive in the nutrient-poor open ocean.

For the Palenik-led paper, contributors included Bianca Brahamsha, Eric Allen, and Jay McCarren of Scripps. Others included researchers from Oak Ridge National Laboratory; the Joint Genome Institute; Lawrence Livermore National Laboratory; TIGR (The Institute for Genomic Research); Centre National de la Recherche Scientifique, Station Biologique de Roscoff in France; and Woods Hole Oceanographic Institution.

Palenik says the paper is the first of a set in a Department of Energy initiative aimed at understanding marine phytoplankton. It is the beginning, Palenik says, of a program that is going to be important for marine science by revealing how photosynthetic organisms fix carbon in the marine environment and adapt to specific habitats within that environment.

In the Palenik-led study, one of the most revealing of many details of the newly sequenced genome was an "enormous" protein found in Synechococcus. Palenik says it is one of the largest bacterial proteins ever reported.

He also says Synechococcus, and not the other three genomes newly reported, can be genetically manipulated. Scripps Marine Biology Research Division scientist Bianca Brahamsha developed a way to remove specific genes to evaluate their functions. When she and Scripps graduate student Jay McCarren removed, or "knocked out," the gene for the large protein, the organism stopped swimming.

"These organisms are known for their unique type of swimming," says Palenik, "and this newly uncovered fact will shed light on how these organisms can convert chemical energy into swimming motion."

Palenik's group further showed that Synechococcus, compared with the other reported organisms, has a broader capability for using different compounds for growth. While the others clearly prefer low-light/high-nutrient or high-light/low-nutrient niches, Synechococcus exhibits "jack-of-all-trades," or generalist, characteristics by using various nitrogen and phosphorous compounds for growth.

Finally, Palenik says the paper shows that Synechococcus displays a history of picking up foreign DNA and converting it into useful genes for its own purposes. Countering the reputation of the open ocean as an isolated, dilute environment, Palenik says this new evidence shows a high volume of organisms interacting with each other and with other viruses.

"It's amazing," said Palenik, "that marine Synechococcus were only discovered in 1978. So in 25 years we've gone from not knowing they were there to suddenly knowing every base pair of DNA." (Prochlorococcus was discovered even later, in 1988.)

Palenik believes such marine genomic information will help in the long run in understanding biodiversity and its conservation.

"We've always been trying to understand how diverse our planet's organisms are," said Palenik. "These results are helping us do that. Starting to decipher whole genomes of different groups of organisms will help us understand how diverse they are and why they are diverse."

In the same issue of Nature, a team led by Gabrielle Rocap of the University of Washington reported extensive differences between the genomes of two strains of Prochlorococcus and helps explain their adaptation to different light and nutrient environments. That study included coauthors from the Massachusetts Institute of Technology (MIT), Oak Ridge National Laboratory, the Joint Genome Institute, Lawrence Livermore National Laboratory, the University of Washington (UW), Humboldt University in Germany, Interuniversity Institute of Marine Science in Israel, and Woods Hole Oceanographic Institution. The Synechococcus and MIT/UW Prochlorococcus teams worked closely together in deciphering their genomes.

In the Proceedings of the National Academy of Sciences paper, a team led by Frederick Partensky of the Centre National de la Recherche Scientifique, Station Biologique de Roscoff, reports on the genome of a third strain of Prochlorococcus.

Coauthors of Palenik's research paper include, in addition to Brahamsha, McCarren, and Allen, Frank Larimer, Miriam Land, Loren Hauser, Patrick Chain, Jane Lamerdin, Wayne Regala, Ian Paulsen, Alexis Dufresne, Frederic Partensky, Eric Webb, and John Waterbury.
Palenik's study was supported by the Biological and Environmental Research Program and the U.S. Department of Energy's Office (DOE) of Science. Additional support was provided by the DOE, the National Science Foundation, and the Margenes program of the European Community.