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MIT reels in RNA surprise with microbial ocean catch
Date:5/24/2009

icrobes to change their protein expression. That same sensitivity makes some of these creatures exceedingly difficult to grow in lab cultures.

To overcome the hurdle of quickly collecting and filtering microbial samples in seawater before the microbes change their protein expression, the research team collaboratively with CEE Professor Sallie (Penny) Chisholm and her research team, which has successfully grown and studied the photosynthetic microbe, Prochlorococcus, in the lab created a method for amplifying the RNA extracted from small amounts of seawater by modifying a eukaryotic RNA amplification technique.

When Shi began lab studies of the RNA in their samples, she found that much of the novel RNA they expected to be protein-coding was actually small RNA (or sRNA), which can serve as a catalyst or regulator for metabolic pathways in microbes.

"What's surprising to me is the abundance of novel sRNA candidates in our data sets," said Shi. "When I looked into the sequences that cannot be confidently assigned as protein-coding, I found that a big percentage of those sequences are non-coding sequences derived from yet-to-be-cultivated microorganisms in the ocean. This was very exciting to us because this metatranscriptomic approach using a data set of sequences of transcripts from a natural microbial community as opposed to a single cultured microbial strain opens up a new window of discovering naturally occurring sRNAs, which may further provide ecologically relevant implications."

"We've found an incredibly diverse set of molecules and each one is potentially regulating a different protein encoding gene," said DeLong. "We will now be able to track the protein expression and the sRNA expression over time to learn the relevance of these little switches."

If we think of marine bacteria and their proteins as tiny factories performing essential biogeochemical activities such as harvesting sunlight to create oxygen and
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Contact: Elizabeth Thomson
thomson@mit.edu
617-258-5402
Massachusetts Institute of Technology
Source:Eurekalert

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