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Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

Zasha Weinberg12*, Joy X Wang1, Jarrod Bogue24, Jingying Yang2, Keith Corbino1, Ryan H Moy25 and Ronald R Breaker123*

Author Affiliations

1 Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA

2 Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA

3 Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA

4 Current address: Department of Biology, University of Rochester, Rochester, NY 14627, USA

5 Current address: School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

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Genome Biology 2010, 11:R31  doi:10.1186/gb-2010-11-3-r31

Published: 15 March 2010

Abstract

Background

Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure.

Results

By applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. Twelve candidate metabolite-binding RNAs were identified, three of which were validated, including one reported herein that binds the coenzyme S-adenosylmethionine. Newly identified cis-regulatory RNAs are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by Helicobacter, and many other physiological processes. A candidate riboswitch termed crcB is represented in both bacteria and archaea. Another RNA motif may control gene expression from 3'-untranslated regions of mRNAs, which is unusual for bacteria. Many noncoding RNAs that likely act in trans are also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences.

Conclusions

This work greatly expands the variety of highly structured noncoding RNAs known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. Given the sustained rate of RNA discovery over several similar projects, we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms.