Identifying novel small RNAs

Researchers have more than doubled the number of identified sRNAs in E. coli

Small RNAs (sRNAs) are important regulatory molecules found in both prokaryotic and eukaryotic cells. Although hundreds of sRNAs are found in eukaryotic cells, only thirteen have been identified in E. coli.

A highly anticipated paper in G&D will add seventeen previously unidentified sRNAs to this list, and provide a starting point for resolving an intriguing biological debate.

Unlike most RNA transcripts which encode proteins, sRNAs are non-coding transcripts � they function directly as RNAs. Eukaryotic sRNAs are largely involved in ribosomal RNA processing and modification. Previously identified prokaryotic sRNAs are involved in a number of cellular processes, but none of which involve ribosomal RNA biogenesis.

This apparent difference between eukaryotic and prokaryotic sRNA functionality has prompted biologists to question whether this difference represents an evolutionary divergence or simply our incomplete knowledge of the full range of prokaryotic sRNA actions.

Dr. Susan Gottesman and colleagues at the National Institutes of Health have developed a systematic method to predict and identify novel sRNAs in the fully sequenced E. coli genome.

As previous genomic screens have overlooked these small non-coding sequences, Dr. Gottesman and colleagues utilized a multifaceted search strategy. By combining comparative genomics, RNA transcript analysis, microarray data and binding activity, the research team was able to minimize oversights and maximize yield.

As published in the July 1 issue of Genes & Development, Dr. Gottesman and colleagues have identified seventeen novel prokaryotic sRNAs. Their experimental methodology serves as a blueprint for the systematic identification of sRNAs in other organisms with sequenced genomes.

Furthermore, the functional characterization of these newly identified sRNAs will lend valuable insight into the debate over whether the apparent differences between eukaryotic sRNA functions and prokaryotic sRNA functions are the result of an evolutionary divergence or our own lack of understanding.