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.
Highlights
Archaeal species are known to encode a plethora of small RNA molecules
Pyrosequencing, followed by selection of uniquely mapped sequence reads, allowed detection of reads associated with both known and novel genomic features (Figure 1), including: (i) small nucleolar RNAs (snoRNAs)-like guide RNAs, including known and novel C/D box small RNA (sRNA) and a new class of H/ACA-like sRNA (Bernick et al, 2012), (ii) RNA sequences encoded cis-antisense to known protein coding genes, (iii) RNA sequences derived from CRISPR arrays, thought to guide the CRISPR-mediated immune response, (iv) unclassified novel sRNA, and (v) degradation products of larger RNA including ribosomal
+− +− Exp Stat P. islandicum classifications were made based on mapping to genes coding for C/D box sRNA (C/D sRNA), H/ACA-like sRNA, CRISPR arrays, fragments of coding regions, ribosomal RNA, and transfer RNA
Summary
Archaeal species are known to encode a plethora of small RNA (sRNA) molecules. These sRNAs have a multitude of functions including suppression of messenger RNA (mRNA; Straub et al, 2009), targeting modifications to ribosomal (rRNA) or transfer RNA (tRNA; Omer et al, 2000; Bernick et al, 2012), specifying targets of the CRISPR immune defense system (Barrangou et al, 2007; Hale et al, 2008; Hale et al, 2009), cis-antisense regulation of transposase mRNA (Tang et al, 2002; Tang et al, 2005; Jager et al, 2009; Wurtzel et al, 2010), and encoding short proteins less than 30 amino acids in length (Jager et al, 2009).Only a few previous studies have described sRNA genes in the phylum Crenarchaeota. In the Sulfolobus genus, C/D box and H/ACA-box guide sRNAs have been studied, including 18 guide sRNAs in Sulfolobus acidocaldarius (Omer et al, 2000), nine in S. solfataricus (Zago et al, 2005), and corresponding homologs detected computationally in S. tokodaii (Zago et al, 2005). These sRNAs form two distinct classes of guide RNAs: C/D box sRNAs which guide 2 -O-methylation of ribose, and H/ACA-box guide RNAs which direct isomerization of uridine to pseudouridine. We employed high-throughput sequencing to identify ten conserved, novel families of H/ACA-like sRNA within the genus Pyrobaculum (Bernick et al, 2012)
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