title: 2'-O-methylation of the wobble residue of elongator pre-tRNA(Met) in Haloferax volcanii is guided by a box C/D RNA containing unique features.
abstract: The wobble residue C34 of Haloferax volcanii elongator tRNA(Met) is 2'-O-methylated. Neither a protein enzyme nor a guide RNA for this modification has been described. In this study, we show that this methylation is guided by a box C/D RNA targeting the intron-containing precursor of the tRNA. This guide RNA is starkly different from its homologs. This unique RNA of approximately 75 bases, named sR-tMet, is encoded in the genomes of H. volcanii and several other haloarchaea. A unique feature of sR-tMet is that the mature RNA in H. volcanii is substantially larger than its predicted size, whereas those in other haloarchaea are as predicted. While the 5'-ends of all tested haloarchaeal sR-tMets are equivalent, H. volcanii sR-tMet possesses an additional 51-base extension at its 3' end. This extension is present in the precursor but not in the mature sR-tMet of Halobacterium sp., suggesting differential 3'-end processing of sR-tMet in these two closely related organisms. Archaeal box C/D RNAs mostly contain a K-loop at the C'/D' motif. Another unique feature of sR-tMet is that its C'/D' motif lacks either a conventional K-turn or a K-loop. Instead, it contains two tandem, sheared G•A base pairs and a pyrimidine-pyrimidine pair in the non-canonical stem; the latter may form an alternative K-turn. Gel shift assays indicate that the L7Ae protein can form a stable complex with this unusual C'/D' motif, suggesting a novel RNA structure for L7Ae interaction.
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL, USA.
authors.forename: Archi
authors.initials: A
authors.lastname: Joardar
authors.forename: Srinivas R
authors.initials: SR
authors.lastname: Malliahgari
authors.forename: Geena
authors.initials: G
authors.lastname: Skariah
authors.forename: Ramesh
authors.initials: R
authors.lastname: Gupta
mesh_terms: D001483:Base Sequence; D019622:Haloferax volcanii / Q000235:genetics* / Q000378:metabolism; D008745:Methylation; D009690:Nucleic Acid Conformation; D012323:RNA Processing, Post-Transcriptional; D019642:RNA, Archaeal / Q000737:chemistry* / Q000235:genetics; D012358:RNA, Transfer, Met / Q000235:genetics*; D017422:Sequence Analysis, DNA; D058727:RNA, Small Untranslated
chemical_list: D019642:RNA, Archaeal; D012358:RNA, Transfer, Met; D058727:RNA, Small Untranslated