Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2012 Jul 12

PMID 22783241

Citations 19

Authors

David L Bernick

Patrick P Dennis

Lauren M Lui

Todd M Lowe

Affiliations

Soon will be listed here.

Abstract

A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea is limited. We employed RNA-seq to identify novel sRNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense sRNAs encoded opposite to key regulatory (ferric uptake regulator), metabolic (triose-phosphate isomerase), and core transcriptional apparatus genes (transcription factor B). We also found a large increase in the number of conserved C/D box sRNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these sRNAs indicates they are relatively recent, stable adaptations.

Citing Articles

Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea.

Gelsinger D, Reddy R, Whittington K, Debic S, DiRuggiero J RNA Biol. 2021; 18(11):1867-1881.

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Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription.

Grunberger F, Reichelt R, Bunk B, Sproer C, Overmann J, Rachel R Front Microbiol. 2019; 10:1603.

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Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species.

Lui L, Uzilov A, Bernick D, Corredor A, Lowe T, Dennis P Nucleic Acids Res. 2018; 46(11):5678-5691.

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Gelsinger D, DiRuggiero J Genes (Basel). 2018; 9(3).

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