Analysis of the Binding of Xenopus Ribosomal Protein L5 to Oocyte 5 S rRNA

Abstract

Xenopus ribosomal protein L5 was expressed in Escherichia coli and exhibits high affinity (K d ‫؍‬ 2 nM) and specificity for oocyte 5 S rRNA. The pH dependence of the association constant for the complex reveals an ionization with a pK a value of 10.1, indicating that tyrosine and/or lysine residues are important for specific binding of L5 to the RNA. Formation of the L5⅐5 S rRNA complex is remarkably insensitive to ionic strength, providing evidence that nonelectrostatic interactions make significant contributions to binding. Together, these results suggest that one or more tyrosine residues may form critical contacts through stacking interactions with bases in the RNA. In order to locate recognition elements within 5 S rRNA, we measured binding of L5 to a collection of site-specific mutants. Mutations in the RNA that affected the interaction are confined to the hairpin structure comprised of helix III and loop C. Earlier experiments with a rhodium structural probe had shown that the two-nucleotide bulge in helix III and the intrinsic structure of loop C create sites in the major groove that are opened and accessible to stacking interactions with the metal complex. In the present studies, we detect a correlation between the intercalative binding of the rhodium complex to mutants in the hairpin and binding of L5, supporting the proposal that binding of the protein is mediated, in some part, by stacking interactions. Furthermore, the results from mutagenesis establish that, despite overlapping binding sites on 5 S rRNA, L5 and transcription factor IIIA utilize distinct structural elements for recognition.The metabolism of Xenopus 5 S ribosomal RNA during oogenesis provides the opportunity to study the interaction of several different proteins with the same nucleic acid. Moreover, these individual ribonucleoprotein complexes appear to determine the intracellular translocation of 5 S rRNA. Initially, the primary transcripts are transiently associated with the La antigen in the nucleus (1, 2). However, the synthesis of 5 S rRNA and ribosome assembly are discontinuous in the early stages of oogenesis, so that much of the RNA is stored in the cytoplasm complexed either with transcription factor IIIA (TFIIIA) 1 or with the protein p43 as part of a large multicomponent 42 S RNP complex (3, 4). Coincident with the expression of the ribosomal proteins during vitellogenesis, an increasing amount of cytoplasmic 5 S rRNA becomes associated with ribosomal protein L5 (5). This latter complex then moves to the nucleolus, where it becomes integrated into nascent ribosomes (1, 6). Mutant forms of 5 S rRNA that are unable to bind to TFIIIA or L5 are retained in the nucleus of the oocyte, indicating that the RNA can only be exported to the cytoplasm in the form of an RNP complex (2). Likewise, the ultimate return of cytoplasmic 5 S rRNA to the nucleolus depends on the formation of the complex with L5 (6, 7). It is not known how the formation of a particular RNP particle creates a signal for nucleocytoplasmic transport.The interacti...

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

“…In fact, the affinity of L5 to 5S rRNA seems to be directly linked to the nucleotides in helix III and loop C (Scripture and Huber 2011). It is interesting to note that in Xenopus, a U 43 → A artificial mutation in loop C, which resulted in a marked decrease in affinity to L5, is identical to the difference between the somatic (U 43 ) and maternal (A 43 ) types in Zebrafish (Scripture and Huber 1995). In Xenopus, the (long) repeats of 45S rRNA transcriptional units are amplified extra-chromosomally during the oogenesis to enable the production of the massive amount of rRNAs needed in the developing embryo (Cohen et al 1999).…”

Characterization of a Novel Association between Two Trypanosome-Specific Proteins and 5S rRNA

“…A point mutant in Loop C was constructed by site-directed mutagenesis (GeneTailor, Invitrogen) at one of the positions (U43) that interferes with binding of the Xenopus L5 protein [17] and with chemical cleavage within loop C [18]. Plasmid pcR2.1Tb5S, which contains the full length rDNA for 5S rRNA, was methylated and subjected to amplification in the presence of an oligonucleotide designed to introduce a single substitution of U at position 43 in Loop C for A. Endonuclease digestion was used to remove the methylated wild type parent plasmid and the amplified plasmid was transformed into E. coli .…”

Stem-loop structure in the 5′ region of potato virus X genome required for plus-strand RNA accumulation

“…Structure probing data of PVX RNA show that LC residues are accessible to DMS and to RNase V 1 , indicating that the LC region of SL1 contains some helical or stacked residues. Because stacking within loops has been found to be important for protein binding in other systems (Scripture & Huber, 1995;Gubser & Varani, 1996), such interactions within LC may additionally be needed for recognition by viral and/or host factors. Alternatively, the sequence requirements in LC may not represent residues critical for contacting protein, but rather be important for establishment of a critical loop structure.…”