Photosynthesizing bacteria with a day-night cycle contain rare ...(lar chromosomes. Linear chromosomes are ...)

Photosynthesis and nitrogen fixation are incompatible, leading this microbe to separate the activities both physically within the cell and temporally, via night and day. While not incompatible, scientists sequencing DNA and those identifying proteins often do their work in separate groups as well.

Proteomics analysis examines almost the whole complement of proteins in a cell, but requires a gene sequence with which to pair up protein shards for identification. On the other hand, DNA sequencing can't always identify potential genes or unmask which of those really function, and could benefit from knowing which proteins the cell actually makes.

Instead of waiting on one analysis to do the other, the collaborators simultaneously sequenced the bacteria's DNA and determined proteins that the microbe produced at different times of its life cycle. They then compared the information to determine which of the DNA sequences that looked like genes actually made proteins. In this way, they could better determine where genes lie along the length of its genome, as well as find ones that might otherwise be missed.

"This was an excellent example of using proteomics to guide initial genomic annotation," said protein chemist Jon Jacobs of PNNL. "We're helping to set a precedent if we can do the proteomics work while they're doing the genomics work."

Overall, Cyanothece 51142 carries one large circular chromosome and four small chromosomes called plasmids, and the linear one. On these, the team found 2,735 genes that looked like genes in other organisms, suggesting they are actual proteins. One important finding was that the unexpected linear chromosome was more than just a pretty face. It contained the only copy of a key protein that lets the bugs produce lactate, called lactate dehydrogenase, during fermentation.

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