The open ocean is teeming with microbial small RNAs that regulate a multitude of environmental processes ranging from carbon metabolism to nutrient acquisition, according to a paper published in tomorrow's (May 14) issue of Nature.

Particle traps like these were used to collect water column samples Image: SOEST/University of Hawaii

"What makes this study quite exciting is the access to novel and previously unidentified small RNAs," Jack Gilbert, a molecular ecologist at the Plymouth Marine Laboratory who was not involved in the study, told The Scientist. "Now we can look at the transcripts and regulation of whole suites of pathways in a whole community."

In 2007, researchers from the J. Craig Venter Institute sailed around the world aboard the Sorcerer II yacht and used metagenomic shotgun sequencing approaches to identify millions of previously unknown protein-coding genes. Then last year, Gilbert and the Massachusetts Institute of Technology's Edward DeLong each independently performed metatranscriptomic analyses to discover slews of new messenger RNA transcripts. Those studies also turned up many RNA sequences that could not be matched to any known protein-coding genes or ribosomal RNAs, indicating that many non-coding regulatory RNAs might literally be swimming through the seas.

Now, DeLong, his graduate student Yanmei Shi, and postdoc Gene Tyson have discovered that around 30% of all RNA transcripts in the North Pacific Ocean code for short, untranslated transcripts that match to the regions between genes in microbial genomes. The study "shows how many more potential small regulatory RNAs are out there," Gisela Storz, a small RNA expert at the National Institute of Child Health and Human Development in Bethesda, MD, who did not contribute to the research findings, told The Scientist. "The next part is the hard part, and that's to figure out what they're doing"

DeLong's team analyzed four depths from an ocean water column in Hawaii, ranging from 25 to 500 meters below sea level. They found some classes of small RNAs universally at all depths, but many of the small RNAs were unique to particular samples and may be derived from as-yet uncharacterized microbes. "We can already see that there are differences between communities and trophic habitats," said DeLong. "But we have a lot more to do to look at the dynamics of small RNA expression and how that relates to protein-coding gene expression."

Researchers have used model laboratory microorganisms to show that small RNAs are involved in regulating important environmental processes including metabolism, quorum sensing, and photosynthesis. To determine whether the novel RNA transcripts were true regulatory small RNAs, DeLong's team looked for matches with known small RNAs, used self-clustering algorithms to group unknown transcripts based on sequence similarity, and compared the RNA folding patterns with known structural motifs. Working out these methods was "not a trivial problem," said DeLong, but "it's a very extensible type of approach." Now, others can use the same techniques to create "biosensors" of environmental perturbations. "Once we start to suss out the patterns [of small RNAs] we might have some pretty powerful markers," he said.


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