title: Binding of a group II intron-encoded reverse transcriptase/maturase to its high affinity intron RNA binding site involves sequence-specific recognition and autoregulates translation.
abstract: Mobile group II introns encode reverse transcriptases that bind specifically to the intron RNAs to promote both intron mobility and RNA splicing (maturase activity). Previous studies with the Lactococcus lactis Ll.LtrB intron suggested a model in which the intron-encoded protein (LtrA) binds first to a primary high-affinity binding site in intron subdomain DIVa, an idiosyncratic structure at the beginning of the LtrA coding sequence, and then makes additional contacts with conserved regions of the intron to fold the RNA into the catalytically active structure. Here, we analyzed the DIVa binding site by iterative in vitro selection and in vitro mutagenesis. Our results show that LtrA binds to a small region at the distal end of DIVa that contains the ribosome-binding site and initiation codon of the LtrA open reading frame. The critical elements are in a small stem-loop structure emanating from a purine-rich internal loop, with both sequence and structure playing a role in LtrA recognition. The ribosome-binding site falls squarely within the LtrA-binding region and is sequestered directly by the binding of LtrA or by stabilization of the small stem-loop or both. Finally, by using LacZ fusions in Escherichia coli, we show that the binding of LtrA to DIVa down-regulates translation. This mode of regulation limits accumulation of the potentially deleterious intron-encoded protein and may facilitate splicing by halting ribosome entry into the intron. The recognition of the DIVa loop-stem-loop structure accounts, in part, for the intron specificity of group II intron maturases and has parallels in template-recognition mechanisms used by other reverse transcriptases.
authors.affiliation: Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, 78712, USA.
authors.forename: Ravindra N
authors.initials: RN
authors.lastname: Singh
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Saldanha
authors.forename: Lisa M
authors.initials: LM
authors.lastname: D'Souza
authors.forename: Alan M
authors.initials: AM
authors.lastname: Lambowitz
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D017930:Genes, Reporter; D014644:Genetic Variation; D007438:Introns; D007763:Lac Operon; D013294:Lactococcus lactis / Q000235:genetics* / Q000378:metabolism*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012326:RNA Splicing; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012194:RNA-Directed DNA Polymerase / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D029701:Saccharomyces cerevisiae Proteins; C066564:aI2 protein, S cerevisiae; C099785:LtrA protein, Lactococcus lactis; D012194:RNA-Directed DNA Polymerase