Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2

PLoS One. 2013 Oct 7;8(10):e76569. doi: 10.1371/journal.pone.0076569. eCollection 2013.


Recent studies identified a 5´ to 3´ exoribonuclease termed Sso-RNase J in the crenarchaeon Sulfolobus solfataricus (Sso), which has been reclassified to the aCPSF2 (archaeal cleavage and polyadenylation specificity factor 2) group of β-CASP proteins. In this study, the Sso-aCPSF2 orthologue of Sulfolobus acidocaldarius (Saci-aCPSF2) was functionally characterized. Like Sso-aCPSF2, Saci-aCPSF2 degrades RNA with 5´ to 3´ directionality in vitro. To address the biological significance of Saci-aCPSF2, a deletion mutant was constructed, and the influence of Saci-aCPSF2 on the transcriptome profile was assessed employing high throughput RNA sequencing. This analysis revealed 560 genes with differential transcript abundance, suggesting a considerable role of this enzyme in RNA metabolism. In addition, bioinformatic analyses revealed several transcripts that are preferentially degraded at the 5´ end. This was exemplarily verified for two transcripts by Northern-blot analyses, showing for the first time that aCPSF2 proteins play a role in 5' to 3' directional mRNA decay in the crenarchaeal clade of Archaea.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaeal Proteins / genetics*
  • Archaeal Proteins / metabolism
  • Blotting, Northern
  • Cleavage And Polyadenylation Specificity Factor / genetics*
  • Cleavage And Polyadenylation Specificity Factor / metabolism
  • Exoribonucleases / genetics*
  • Exoribonucleases / metabolism
  • Gene Expression Regulation, Archaeal*
  • Genes, Archaeal / genetics
  • Molecular Sequence Data
  • Mutation
  • RNA Stability
  • RNA, Archaeal / genetics
  • RNA, Archaeal / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Homology, Amino Acid
  • Sulfolobus acidocaldarius / genetics*
  • Sulfolobus acidocaldarius / metabolism
  • Transcriptome*


  • Archaeal Proteins
  • Cleavage And Polyadenylation Specificity Factor
  • RNA, Archaeal
  • RNA, Messenger
  • Exoribonucleases