Monday, April 30, 2007
First Genome Comparison of Plankton Species
Yields Surprises Underlying Key Ocean Processes
Prominent evidence of selenium use by microbes may force new ideas of element's role in planetary processes such as carbon cycling and photosynthesis
Scripps Institution of Oceanography / University of California, San DiegoAn international team of scientists led by Scripps Institution of Oceanography at UC San Diego and the Department of Energy's (DOE) Joint Genome Institute has peered into the genetic makeup of two species of phytoplankton, the tiny plants key in global photosynthesis and carbon cycling, and come away with surprising results about evolutionary engineering and new ideas about the role that a poorly understood chemical element may play in the world's oceans.
For several years, Scripps Oceanography's Brian Palenik and his collaborators, including scientists from France, Belgium and Germany, have been analyzing and annotating an organism called Ostreococcus. At one micron it is the smallest known phytoplankton and one of the smallest of all the eukaryotes, organisms with specialized internal cell structures that include plants and animals. A teaspoon of seawater taken off the Scripps Oceanography Pier typically contains more than 100,000 eukaryotic phytoplankton, which are found throughout the world's oceans. Phytoplankton are responsible for nearly half of the planet's photosynthesis.
Advances in genomics have allowed scientists to begin digging deeply into a long-standing biological puzzle concerning the mechanisms behind the divergent genomes of related photosynthetic phytoplankton species. The international team's work, published in the online edition of Proceedings of the National Academy of Sciences, is the first comparison of the genetic makeup of two closely related eukaryotic phytoplankton and the mechanisms that make them biologically similar and distinct.
"Through our research we've been trying to understand Ostreococcus' role in marine ecosystems," said Palenik, who indicated Ostreococcus cells contain nearly five times the DNA of comparably sized organisms such as cyanobacteria. "Genomics has taught us that you can learn much more when you can do a comparison.. The first genome is exciting but the second genome is even more exciting because you can suddenly compare organisms and see what each is doing differently and what they are doing the same."
A close up of the marine phytoplankton Ostreococcus
The researchers' comparison of Ostreococcus lucimarinus (recently sequenced by the DOE's Joint Genome Institute) and Ostreococcus tauri yielded several surprising results, including the documentation of a "new" chromosome differing between the species. Another chromosome appeared somewhat different between the species and the researchers believe it may serve as a gene transfer "trash can" where foreign DNA is integrated. Yet another difference was the identification of a chromosome featuring the same-albeit rearranged-genes in the two species. The researchers hypothesize that this chromosome may be related to sexual functions because the rearrangements are enough to prevent sex between the species.
"These are pretty remarkable differences that we didn't expect," said Palenik, a professor in the Marine Biology Research Division at Scripps. "We would expect the DNA to change slowly and see a small number of differences between the two species as they slowly evolve... This is the case for much of the genome. From a future applied perspective, from our comparison we are learning the tricks nature has used to 'engineer' an extremely small eukaryotic cell. This may have future applications in bioengineering."
Another important finding described in the paper is the prominent role that the element selenium plays in Ostreococcus. Humans require selenium in small amounts and most people have roughly 25 selenium proteins. Tiny Ostreococcus organisms were shown to have up to 21 selenium proteins, an enormous number relative to their small genome and microscopic size.
Palenik believes this may be because selenium enzymes are some 10- to 50-times more efficient than similar enzymes that don't use selenium. Based on their size, such efficiency is important to help conserve resources such as nitrogen.
"We may need to think more about how selenium helps drive the health of the oceans," said Palenik. "It's a nutrient element that we don't understand very well and now we have evidence of a group of organisms that clearly use it intensively. We may need to think about how this is affecting primary production in the oceans."
Future research by Palenik and his colleagues will involve a third Ostreococcus organism, which will lead to further comparisons and evolutionary evaluations.
"Genomic comparisons are exciting because they allow us not to just document the diversity of the ocean but to start to understand the processes behind that diversity and see all of the changes in the evolution of two species," said Palenik.
Coauthors of the paper include Chris Dupont, Vera Tai, Sheila Podell and Terry Gaasterlandof Scripps; Jane Grimwood and Jeremy Schmutz of Stanford University School of Medicine; Andrea Aerts, Asaf Salamov, Nicholas Putnam, Kemin Zhou, Robert Otillar, Gregory Werner, Inna Dubchak, Daniel Rokhsar and Igor V. Grigoriev of the DOE's Joint Genome Institute; Pierre Rouze, Stephane Rombauts, Steven Robbens and Yves Van de Peer of Ghent University; Richard Jorgensen, Carolyn Napoli and Karla Gendler of the University of Arizona at Tucson; Evelyne Derelle, Gwenael Piganeau, Séverine Jancek and Hervé Moreau of the Université Pierre et Marie Curie Paris 6; Sabeeha Merchant of the University of California, Los Angeles; Olivier Vallon of the Université Paris 6; Andrea Manuell of The Scripps Research Institute; Martin Lohr Johannes of Gutenberg-Universität; Gregory Pazour of the University of Massachusetts Medical School; Marc Heijde, Kamel Jabbari and Chris Bowler of the Centre National de la Recherche Scientifique; Qinghu Ren and Ian Paulsen of The Institute for Genomic Research; and Chuck Delwiche of the University of Maryland at College Park.
The research was supported by the DOE, the European network "Marine Genomics Europe" and performed under the auspices of the DOE's Office of Science, Biological and Environmental Research Program, the University of California, Lawrence Livermore National Laboratory, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory and Stanford University.
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Scripps Institution of Oceanography, at University of California, San Diego, is one of the oldest, largest and most important centers for global science research and education in the world. The National Research Council has ranked Scripps first in faculty quality among oceanography programs nationwide Now in its second century of discovery, the scientific scope of the institution has grown to include biological, physical, chemical, geological, geophysical and atmospheric studies of the earth as a system. Hundreds of research programs covering a wide range of scientific areas are under way today in 65 countries. The institution has a staff of about 1,300, and annual expenditures of approximately $155 million from federal, state and private sources. Scripps operates one of the largest U.S. academic fleets with four oceanographic research ships and one research platform for worldwide exploration.
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