Bioinformatický seminár

Tue 15 Feb. 2011, 17:20

Title: Weinberg et al. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Speaker: Tomáš Vinař

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