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Genome analysis of marine microbe reveals a metabolic minimalist
Date:2/21/2010

f the photosynthetic apparatus <http://press.ucsc.edu/text.asp?pid=2555>. The missing parts, known as photosystem II, carry out the stage in photosynthesis that generates oxygen by splitting water molecules. This is significant because oxygen inhibits nitrogen fixation. Most nitrogen-fixing cyanobacteria carry out photosynthesis during the day and nitrogen fixation at night, but UCYN-A can fix nitrogen all day long.

The new paper extends the list of UCYN-A's missing metabolic pathways to include, among other things, a process central to aerobic metabolism known as the TCA cycle or Krebs cycle. It also lacks the Calvin cycle, which uses the carbon from carbon dioxide to build sugars, and it is unable to synthesize about half of the 20 essential amino acids.

"This thing is really stripped down," said James Tripp, a bioinformatics specialist at UCSC and lead author of the Nature paper. "My analysis indicates it has to have an outside source to obtain sugars, amino acids, and two out of the four bases needed to make DNA."

Tripp performed the genome analysis reported in the paper. He worked closely with scientists at 454 Life Sciences, a Roche company based in Branford, Conn., that specializes in high-throughput DNA sequencing technology. The researchers applied new genome sequencing and assembly techniques to produce the complete genome sequence from natural samples of DNA. Because UCYN-A cannot be cultured, researchers used a cell-sorting technique called flow cytometry to obtain concentrated samples of the microbe from ocean water, and then extracted DNA from the cells for sequencing.

Although UCYN-A must depend on other organisms for key nutrients, the researchers have found no evidence that it lives in a close symbiotic association with another microorganism. Zehr said the failure to find another organism closely associated with it suggests two possibilities. "It might l
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Contact: Tim Stephens
stephens@ucsc.edu
831-459-2495
University of California - Santa Cruz
Source:Eurekalert

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