title: Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2.
abstract: 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.
authors.affiliation: Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria.
authors.forename: Birgit
authors.initials: B
authors.lastname: Märtens
authors.forename: Fabian
authors.initials: F
authors.lastname: Amman
authors.forename: Salim
authors.initials: S
authors.lastname: Manoharadas
authors.forename: Lukas
authors.initials: L
authors.lastname: Zeichen
authors.forename: Alvaro
authors.initials: A
authors.lastname: Orell
authors.forename: Sonja-Verena
authors.initials: SV
authors.lastname: Albers
authors.forename: Ivo
authors.initials: I
authors.lastname: Hofacker
authors.forename: Udo
authors.initials: U
authors.lastname: Bläsi
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D015152:Blotting, Northern; D039223:Cleavage And Polyadenylation Specificity Factor / Q000235:genetics* / Q000378:metabolism; D005095:Exoribonucleases / Q000235:genetics* / Q000378:metabolism; D019848:Gene Expression Regulation, Archaeal; D019766:Genes, Archaeal / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D020871:RNA Stability; D019642:RNA, Archaeal / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D016945:Sulfolobus acidocaldarius / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D019843:Archaeal Proteins; D039223:Cleavage And Polyadenylation Specificity Factor; D019642:RNA, Archaeal; D012333:RNA, Messenger; D005095:Exoribonucleases