Intron and RNA splicing in Archaea

Abstract In Archaea, almost all introns in pre-tRNA, pre-rRNA, and pre-mRNA are spliced through two common steps by protein enzymes: cleavage of the precursor with splicing endonuclease, and ligation of the exons with RNA ligase. We found the first examples of archaeal pre-mRNA splicing and cleavage of the pre-mRNA with a novel subclass of archaeal splicing endonuclease. We further solved the novel tertiary structure of the splicing endonuclease, and revealed that the lineage-specific insertion of amino acid residues in the endonuclease expands the recognition of the substrate precursor RNA. We also discuss the possible involvement of tRNA splicing and its machinery in the origin of the tRNA molecule. (Keywords) intron, RNA splicing, Archaea, splicing endonuclease, RNA ligase, bulge-helix-bulge motif Introduction In bacteria and eukaryotes, some types of RNA splicing occur by precursor RNAs themselves, or with the aid of trans-factors including RNA-protein complexes [1]. However, in Archaea, with a few exceptions of group II introns found in Euryarchaeota [2], almost all of the introns in pre-tRNA [3], pre-rRNA [4], and pre-mRNA [5] are thought to be spliced through two steps catalyzed by protein-based enzymes: cleavage at exon-intron boundaries in precursor RNA with splicing endonuclease The splicing endonuclease recognizes a specific structure in the substrate precursor RNA bulge-helix-bulge (BHB) motif, composed of a 4-basepair central helix flanked by two 3-base bulge loops at the 3' sides together with basepairs, and cleaves the specific sites in the "bulge" region [8, The recently identified archaeal RNA ligase [11] shares a common ancestor with a bacterial RNA repair enzym

eEF1A binding to aminoacylated viral RNA represses minus strand synthesis by TYMV RNA-dependent RNA polymerase

AbstractThe genomic RNA of Turnip yellow mosaic virus (TYMV) has an 82-nucleotide-long tRNA-like structure at its 3′-end that can be valylated and then form a stable complex with translation elongation factor eEF1A·GTP. Transcription of this RNA by TYMV RNA-dependent RNA polymerase (RdRp) to yield minus strands has previously been shown to initiate within the 3′-CCA sequence. We have now demonstrated that minus strand synthesis is strongly repressed upon the binding of eEF1A·GTP to the valylated viral RNA. eEF1A·GTP had no effect on RNA synthesis templated by non-aminoacylated RNA. Higher eEF1A·GTP levels were needed to repress minus strand synthesis templated by valyl-EMV TLS RNA, which binds eEF1A·GTP with lower affinity than does valyl-TYMV RNA. Repression by eEF1A·GTP was also observed with a methionylated variant of TYMV RNA and with aminoacylated tRNAHis, tRNAAla, and tRNAPhe transcripts. It is proposed that minus strand repression by eEF1A·GTP binding occurs early during infection to help coordinate the competing translation and replication functions of the genomic RNA