Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus

doi:10.1073/pnas.112047299

Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobusfulgidus

^*Institute of Experimental Pathology, Von-Esmarch-Strasse 56, 48149 Münster, Germany; ^†Laboratoire de Biologie Moléculaire Eukaryote du Centre National de la Recherche Scientifique, Université Paul-Sabatier, 31062 Toulouse, France; ^§Lehrstuhl für Mikrobiologie, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany; ^¶Max-Planck-Institut für Molekulare Genetik, Harnackstrasse 23, 14195 Berlin, Germany; and ^‖RessourcenZentrum/PrimärDatenbank Deutsches Ressourcenzentrum für Genomforschung GmbH, Heubnerweg 6, 14059 Berlin, Germany

Edited by Norman R. Pace, University of Colorado, Boulder, CO, and approved April 9, 2002 (received for review January 28, 2002)

Abstract

In a specialized cDNA library from the archaeon Archaeoglobus fulgidus we have identified a total of 86 different expressed RNA sequences potentially encoding previously uncharacterized small non-messenger RNA (snmRNA) species. Ten of these RNAs resemble eukaryotic small nucleolar RNAs, which guide rRNA 2′-O-methylations (C/D-box type) and pseudouridylations (H/ACA-box type). Thereby, we identified four candidates for H/ACA small RNAs in an archaeal species that are predicted to guide a total of six rRNA pseudouridylations. Furthermore, we have verified the presence of the six predicted pseudouridines experimentally. We demonstrate that 22 snmRNAs are transcribed from a family of short tandem repeats conserved in most archaeal genomes and shown previously to be potentially involved in replicon partitioning. In addition, four snmRNAs derived from the rRNA operon of A. fulgidus were identified and shown to be generated by a splicing/processing pathway of pre-rRNAs. The remaining 50 RNAs could not be assigned to a known class of snmRNAs because of the lack of known structure and/or sequence motifs. Regarding their location on the genome, only nine were located in intergenic regions, whereas 33 were complementary to an ORF, five were overlapping an ORF, and three were derived from the sense orientation within an ORF. Our study further supports the importance of snmRNAs in all three domains of life.

Footnotes

↵ ‡ To whom reprint requests may be addressed. E-mail: huttenh{at}uni-muenster.de or bachel{at}ibcg.biotoul.fr.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The sequences reported in this paper have been deposited in the DDBJ/EMBL/GenBank databases (accession nos. AJ430234–AJ430319).
Abbreviations:

snmRNA,

small non-mRNA;

snoRNAs,

small nucleolar RNAs;

sRNA,

small RNA