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

Weinberg, Zasha, Wang, Joy X, Bogue, Jarrod, Yang, Jingying, Corbino, Keith, Moy, Ryan H, Breaker, Ronald R·2010·Genome Biology
DOI 10.1186/gb-2010-11-3-r31PMC PMC2864571
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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.

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  • First evidence of molecular mechanism for bacterial resistance to fluoride was discovery of widespread family of fluoride-responsive riboswitches, found upstream of genes predicted to encode halide-specific membrane channels.

    “The first evidence of a molecular mechanism for bacterial resistance to fluoride was the discovery of a widespread family of fluoride-responsive riboswitches, found upstream of genes predicted to encode halide-specific membrane channels (170–172).”

    From Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances (2024) · cites this paper as [171]

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Metadata

Authors
Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R.
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2010-03-15
Volume
11
Issue
3
ISSN
1474-760X
DOI
10.1186/gb-2010-11-3-r31
PMC
PMC2864571
Cited by
354
References
2
Language
en
Licence

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