%0 Journal Article
%T Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
%A Zasha Weinberg
%A Joy X Wang
%A Jarrod Bogue
%A Jingying Yang
%A Keith Corbino
%A Ryan H Moy
%A Ronald R Breaker
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-3-r31
%X 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.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.Ongoing efforts to identify and characterize various structured noncoding RNAs from bacteria are revealing the remarkable functions that structured RNAs can perform [1-3]. To detect novel RNA classes in bacteria and archaea, a variety of bioinformatics strategies have been used [4-12]. In our recent efforts to identify novel structured RNAs, we applied a scheme based on detecting RNA secondary structures upstream of homologous protein-coding genes [13,14]. However, this strategy is best suited to finding cis-regulatory RNAs, not noncoding RNAs. Also, some cis-regulatory RNAs such as c-di-GMP riboswitches [14,15] or ydaO motif RNAs [5] ar
%U http://genomebiology.com/2010/11/3/R31