Human Y5 RNA specializes a Ro ribonucleoprotein for 5S ribosomal RNA quality control

Abstract

Humans express four distinct non-protein-coding Y RNAs (ncRNAs). To investigate Y RNA functional diversification, we exploited an RNA-based affinity purification method to isolate ribonucleoproteins (RNPs) assembled on individual human Y RNAs. Silver staining and mass spectrometry revealed that the Ro and La proteins assemble with all Y RNAs, while additional proteins associate with specific Y RNAs. Unexpectedly, Y5 RNA uniquely copurified ribosomal protein L5 and its binding partner 5S RNA. These findings reveal a contribution of Y5 to 5S surveillance and suggest that interactions between Ro-Y5 and L5-5S RNPs establish 5S RNA as a target of quality control.Supplemental material is available at http://www.genesdev.org.Received August 13, 2007; revised version accepted October 11, 2007. Empirical and computational approaches have revealed a dramatically expanded complexity of non-protein-coding RNA (ncRNA) in higher eukaryotes (Taft et al. 2007). Here we show that individual human Y RNAs have unique protein and ncRNA interaction specificities. We demonstrate that all four human Y RNAs (Y1, Y3, Y4, and Y5) assemble with the core Y RNP proteins Ro and La, and additional proteins exhibit specific interactions with subsets of Y RNPs. Of the human Y RNAs, only Y5 copurifies ribosomal protein L5 and an extensively characterized target of Ro-mediated quality control, 5S ribosomal RNA. We propose that Y RNAs play both positive and negative roles in establishing the target specificity of ncRNA surveillance by Ro. Our findings provide new insights about the functions of ncRNA and the significance of expansion of vertebrate ncRNA diversity. Results and Discussion RNA-based affinity purification of individual Y RNPsAn RNA-based method of affinity purification was required to separate the RNPs endogenously assembled on human Y1, Y3, Y4, and Y5 RNAs. For this purpose, we developed an RNP purification method termed RNA Affinity in Tandem (RAT). Each Y RNA was expressed in vivo as a fusion to an affinity tag composed of two hairpins: one binding the Pseudomonas phage 7 (PP7) coat protein (CP) and one binding the antibiotic tobramycin (Hogg and Collins 2007). Each Y RNA was tagged at the 5Ј or 3Ј end with one or both orientations of the tag hairpins and expressed under the control of the commonly exploited human U6 RNA Polymerase III promoter by transient transfection of human 293T cells. The most uniform Y RNA expression levels were obtained using a 3Ј tag with the PP7 hairpin followed by the tobramycin hairpin (data not shown). Cells expressing the entire panel of Y RNAs with this tag configuration and a parallel empty vector control were lysed to generate whole-cell extracts. Recombinant PP7CP tagged with the two Protein A domains (ZZ) and Tobacco Etch Virus (TEV) protease cleavage site of the protein tandem affinity purification (TAP) tag (Puig et al. 2001) was added to cell extract, and complexes harboring tagged RNA were recovered on IgG agarose. Following elution by TEV protease, tagged RNPs were bound to tobramycin re...

A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication

“…Several proteins and RNPs have been reported to interact with this domain in different Y RNAs, including nucleolin, hnRNP K, hnRNP I, and 5S RNP (Fabini et al 2001;Fouraux et al 2002;Hogg and Collins 2007). These interactions do not occur with all Y RNAs (Fabini et al 2000(Fabini et al , 2001Fouraux et al 2002).…”

“…Functions for Ro60 have been implicated in cellular responses to cytotoxic stress (Labbe et al 2000;Chen et al 2003), in a quality control for small RNAs (Chen and Wolin 2004;Stein et al 2005;Fuchs et al 2006;Chen et al 2007;Hogg and Collins 2007), the export of associated RNAs from the nucleus (Simons et al 1996), and the protection of associated RNAs from exonucleolytic degradation (Chen and Wolin 2004). In vertebrates, the binding site for Ro60 is adjacent to the domain essential for DNA replication, and thus insulates it from the 59 and 39 ends of the RNA.…”

Crystal structure and nucleotide selectivity of human IFIT5/ISG58

“…From an evolutionary point of view, human ISG58 is different from all the other ISG56 family members: it does not have a mouse homologue, and is the only ISG56 family protein so far identified in birds, marsupials, frogs and fish [5]. ISG58 was found to copurify with a diverse mixture of small RNAs consisting mainly of a subset of tRNAs, and a number of noncoding RNAs [6].…”

“…It was previously reported that ISG58 associates with small RNAs in pull-down assays [6], indicating that it can interact directly or indirectly with nucleotides. Our structural study shows that positively-charged residues including lysines and arginines are enriched at the inner surface of the "V"-like structure ( Figure 1B).…”

The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA

“…In vertebrate cells, Ro traffics between nuclear and cytoplasmic compartments. In some nuclei, Ro binds misfolded noncoding RNAs and is proposed to function in noncoding RNA quality control (O'Brien and Wolin 1994;Shi et al 1996;Labbe et al 1999;Chen et al 2003;Hogg and Collins 2007). In the cytoplasm, Ro is bound to z100-nt noncoding RNAs called Y RNAs.…”