Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

Abstract

Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the pathogenic filamentous fungus Aspergillus fumigatus. To that aim, we experimentally screened for ncRNAs, expressed under various growth conditions or during specific developmental stages, by generating a specialized cDNA library from size-selected small RNA species. Our screen revealed 30 novel ncRNA candidates from known ncRNA classes such as small nuclear RNAs (snRNAs) and C/D box-type small nucleolar RNAs (C/D box snoRNAs). Additionally, several candidates for H/ACA box snoRNAs could be predicted by a bioinformatical screen. We also identified 15 candidates for ncRNAs, which could not be assigned to any known ncRNA class. Some of these ncRNA species are developmentally regulated implying a possible novel function in A. fumigatus development. Surprisingly, in addition to full-length tRNAs, we also identified 5′- or 3′-halves of tRNAs, only, which are likely generated by tRNA cleavage within the anti-codon loop. We show that conidiation induces tRNA cleavage resulting in tRNA depletion within conidia. Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus.

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

“…Below the mature tRNA bands, there are additional bands of intermediate size (35-60 nt long) that could correspond to the tRNA cleavage products that were reported recently (Lee and Collins 2005;Haiser et al 2008;Jochl et al 2008;Kawaji et al 2008;Li et al 2008;Thompson et al 2008;Zhang et al 2009). tRF-1001 was also measured by splinted ligation assays (Supplemental Fig.…”

“…tRNA fragments of 30-35 nt have been identified in bacteria, fungi, plants, and animals (Lee and Collins 2005;Haiser et al 2008;Jochl et al 2008;Kawaji et al 2008;Li et al 2008;Thompson et al 2008;Zhang et al 2009). These tRNA fragments are different from the ones reported here in that they are derived from a cleavage at or around the anti-codon loop by Rny1p in yeast (Thompson and Parker 2009) or angiogenin in humans (Yamasaki et al 2009).…”

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability

“…Computational and experimental analysis discovered C/D-box and H/ACA-box small nucleolar RNAs (snoRNAs) with predicted functions in ribosomal RNA maturation in Sulfolobus sulfataricus, S. acidocaldarius, Archaeaglobus fulgidus, and Pyrococcus (11-14), as well as stable antisense RNAs and sRNA species from intergenic regions (IGRs), which are likely to be involved in posttranscriptional control of gene expression (15-18). More recently, several dozen sRNAs were predicted in the high salt-adapted species Haloferax volcanii (19).Although all previous experimental approaches in archaea relied on cDNA cloning followed by Sanger sequencing, highthroughput sequencing of cDNA ] has now revolutionized transcriptome analysis and sRNA discovery in many organisms (21)(22)(23). In the present work we used a recently developed differential RNA-seq method selective for newly initiated transcripts.…”

“…Although all previous experimental approaches in archaea relied on cDNA cloning followed by Sanger sequencing, highthroughput sequencing of cDNA ] has now revolutionized transcriptome analysis and sRNA discovery in many organisms (21)(22)(23). In the present work we used a recently developed differential RNA-seq method selective for newly initiated transcripts.…”

Qipgene inFusarium oxysporumis required for normal hyphae morphology and virulence

“…Based on their RNA precursors and biogenesis mechanisms, these small RNAs can be divided into various types in fungi, including QDE-2-interacting small RNAs (qiRNAs), microRNA-like RNAs (milRNAs), Dicer-independent small interfering RNAs (disiRNAs), small interfering RNAs (siRNAs), long terminal repeat retrotransposon-siRNAs (LTR-siRNAs) and tRNA-derived RNA fragments (tRFs) (Jöchl et al 2008; Lee et al 2009; Nicolas et al 2010; Nunes et al 2011). The maturation of small RNAs in the RNA-silencing pathway is dependent on the RNase III ribonuclease Dicer, RNA-dependent RNA polymerases (RdRps) and Argonaute proteins (Lee et al 2010).…”