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Researchers Merge Sequencing, Proteomics to Analyze Nitrogen-Fixing Cyanobacterium

NEW YORK (GenomeWeb News) – A newly available genome sequence is revealing the unexpected genomic structure of a nitrogen-fixing cyanobacterium, or blue-green algae — and providing clues about how the organism temporally separates its functions.
 
A team of American researchers combined sequencing and proteomics approaches to begin characterizing the genome of a marine cyanobacterial species called Cyanothece sp. 51142, an organism that photosynthesizes by day and fixes nitrogen by night. The results, scheduled to appear online this week in the Proceedings of the National Academy of Sciences, reveal key Cyanothece 51142 genetic pathways and uncover a genomic first for cyanobacteria — a linear chromosome.
 
“Now, we have the genome of this organism, which gives us a complete picture of everything that can possibly happen in this cell,” senior author Himadri Pakrasi, a biologist at Washington University in St. Louis, said in a statement. “The way the cell prospers, multiplies and dies is all decided in the genome.”
 
Cyanobacteria are single-celled organisms that share features with both plants and microbes. For example, Cyanothece 51142 produces sugars via photosynthesis during the day. At night, it expresses genes involved in metabolism and respiration, as well as those needed for nitrogen fixation, the process of converting atmospheric nitrogen to a biologically accessible form.
 
Because it can produce ethanol and hydrogen, Cyanothece 51142 is also of interest for those researching alternative fuel sources.
 
For this paper, researchers at the Washington University Genome Sequencing Center used an Applied Biosystems 3730 to sequence the roughly 5.5 million base pair Cyanothece 51142 genome.
 
When they and their colleagues analyzed this genome, they found that it is comprised of six parts: a circular chromosome of about 4.9 million bases, four circular plasmids ranging from about ten to 40 thousand bases, and — unexpectedly — a 429,701 base pair linear chromosome.
 
“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.”
 
By coupling their sequencing efforts with proteomics analysis, the researchers were able to not only identify new genes but also get a much clearer picture of which genes are expressed by Cyanothece 51142.
 
“This was an excellent example of using proteomics to guide initial genomic annotation,” co-author Jon Jacobs, a systems biologist at the Pacific Northwest National Laboratory, said in a statement. “We’re helping to set a precedent if we can do the proteomics work while they’re doing the genomics work.”
 
“Using proteomics, we always suspected we’d be able to detect genes not called out in the genome,” Jacobs continued, “but it was surprising how many hypothetical genes actually produced proteins.”
 
The team identified 2,735 protein-coding genes, plus another 506 protein-coding genes originally classified as hypothetical genes. They also picked out highly conserved gene clusters involved in nitrogen fixation and glucose metabolism and fingered the genes and pathways used for fermentation and metabolic storage.
 
Analyzing the linear chromosome was similarly informative. The chromosome contained a cluster of nine genes coding for enzymes involved in lactate fermentation — including the lone copy of the gene for the enzyme lactate dehydrogenase.
 
Together, these findings provide new insights into Cyanothece 51142 genome organization, providing a peak into the strategies that the cyanobacterium uses to fix nitrogen, separate its dark and light activities, and produce energy and fermentation products such as ethanol, lactate, acetate, and hydrogen.
 
“These genome-based insights highlight the overall strategy of Cyanothece 51142 to maximize efficiency by tightly regulating major metabolic processes throughout a diurnal cycle,” the authors wrote.
 
In an effort to gain a more comprehensive understanding of Cyanothece functions — and particularly hydrogen production — the team is currently sequencing six additional Cyanothece strains isolated from the deep ocean and from rice paddies in Taiwan and India. “The goal is to find the hydrogen-producing workhorse of these seven,” Pakrasi explained.

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