Ro60 and Y RNAs: structure, functions, and roles in autoimmunity

Abstract

Ro60, also known as SS-A or TROVE2, is an evolutionarily conserved RNA-binding protein that is found in most animal cells, approximately 5% of sequenced prokaryotic genomes and some archaea. Ro60 is present in cells as both a free protein and as a component of a ribonucleoprotein complex, where its best-known partners are members of a class of noncoding RNAs called Y RNAs. Structural and biochemical analyses have revealed that Ro60 is a ring-shaped protein that binds Y RNAs on its outer surface. In addition to Y RNAs, Ro60 binds misfolded and aberrant noncoding RNAs in some animal cell nuclei. Although the fate of these defective Ro60-bound noncoding RNAs in animal cells is not well-defined, a bacterial Ro60 ortholog functions with 3' to 5' exoribonucleases to assist structured RNA degradation. Studies of Y RNAs have revealed that these RNAs regulate the subcellular localization of Ro60, tether Ro60 to effector proteins and regulate the access of other RNAs to its central cavity. As both mammalian cells and bacteria lacking Ro60 are sensitized to ultraviolet irradiation, Ro60 function may be important during exposure to some environmental stressors. Here we summarize the current knowledge regarding the functions of Ro60 and Y RNAs in animal cells and bacteria. Because the Ro60 RNP is a clinically important target of autoantibodies in patients with rheumatic diseases such as Sjogren's syndrome, systemic lupus erythematosus, and neonatal lupus, we also discuss potential roles for Ro60 RNPs in the initiation and pathogenesis of systemic autoimmune rheumatic disease.

Keywords: RNA degradation; Ro60; Rsr; Y RNA; autoantigen; noncoding RNA.

Figure 1

Crystal structures of Ro60 and its bacterial ortholog Rsr. Structures of (A) X. laevis Ro60 (PDB 1YVR) and (B) D. radiodurans Rsr (PDB 2NVO), colored from the N-terminus in bright blue to the C- terminus in cyan (see color version of this figure at www.tandfonline.com/ibmg).

Figure 2

Secondary structures of Y RNAs. (A) The four human Y RNAs. The Ro60-binding module is within a stem formed by pairing the 5’ and 3’ portions of each Y RNA. Boxed regions indicate sequences that are conserved among all characterized animal cell Y RNAs and are important for Ro60 binding. Structure-probing experiments (Green CD et al. 1998) indicate that this portion of the stem can exist in two conformations (arrow). In the crystal structure of X. laevis Ro60 complexed with Y3 RNA (Stein et al. 2005), nucleotides colored magenta are sites of base-specific interactions with Ro60. The effector binding/cavity-gating module of Y RNAs differs between individual Y RNAs, which may allow for interactions with different effectors. (B) D. radiodurans Yrn1 (Y RNA 1) and Yrn2 RNAs. (C) S. Typhimurium YrlA and YrlB RNAs. The Rsr binding sites in Yrl RNAs diverge from those of metazoan Y RNAs and bacterial Yrn RNAs and have the consensus sequence GNCGAAN_0–1G (green), in which the CGA may correspond to the CGA at the end of the metazoan motif (Sim and Wolin 2018) (see color version of this figure at www.tandfonline.com/ibmg).

Figure 3

YrlA RNAs are tRNA mimics. (A). S. Typhimurium YrlA drawn to resemble tRNA. The positions of the D and T arms are indicated, as are the acceptor stem (AS), variable loop (V) and anticodon stem (AC). The indicated nucleotides were shown to be modified to dihydrouridine (D) and pseudouridine (Ψ) in vivo (Chen et al. 2014). The boxed region was crystallized. (B) Crystal structure of the effector-binding domain of YrlA (PDB 6CU1). (C) Structure of Saccharomyces cerevisae tRNA^Phe (PDB 4TNA) (see color version of this figure at www.tandfonline.com/ibmg).

Figure 4

Single particle reconstruction of the RYPER complex at 25 Å (EMDB ID: EMD-5389). The docking of atomic models of S. antibioticus PNPase (PDB 1E3P) and X. laevis Ro complexed with Y RNA (PDB 1YVP) and misfolded RNA (PDB 2I91) into this volume supports a model in which the regions colored in yellow, red and green represent Rsr, Y RNA and PNPase respectively (Chen et al. 2013) (see color version of this figure at www.tandfonline.com/ibmg).

Figure 5

Model for the ways in which Ro60 and Y RNA can function. (A) Ro60 can function as a Y RNA-free protein. This form of Ro60 binds pre-5S RNAs in X. laevis oocyte nuclei and is required for efficient pre-23S rRNA maturation in D. radiodurans (O’Brien and Wolin 1994; Chen et al. 2007). (B) A bound Y RNA can block access of other RNAs to Ro60. Y RNA prevents binding of misfolded pre-5S rRNA to purified Ro60 (Green CD et al. 1998) and inhibits pre-23S rRNA maturation in D. radiodurans (Chen et al. 2007). (C) Y RNAs can act as sponges to sequester other RNA binding proteins. Y3 RNA interacts with nELAVL proteins, potentially preventing these proteins from binding their intended RNA targets (Scheckel et al. 2016; Tebaldi et al. 2018). Whether Ro60 is part of these complexes is unknown. (D) Y RNAs can tether Ro60 to effector proteins, creating RNPs with altered function. In D. radiodurans, Ro60 is tethered to PNPase via Y RNA to form RYPER, which has enhanced activity in degrading structured RNA, compared with PNPase alone (Chen et al. 2013). (E) Y RNAs can tether Ro60 to regulatory proteins. Tethering of Ro60 to ZBP1 by Y3 RNA facilitates nuclear export of the Ro60/Y3 complex (Sim et al. 2012) Although two or more of these states (A-E) can occur within the same cell, the specific state(s) that predominate may differ between cell types and can change in response to stress (see color version of this figure at www.tandfonline.com/ibmg).