The RtcB RNA ligase is an essential component of the metazoan unfolded protein response

Abstract

RNA ligation can regulate RNA function by altering RNA sequence, structure and coding potential. For example, the function of XBP1 in mediating the unfolded protein response requires RNA ligation, as does the maturation of some tRNAs. Here, we describe a novel in vivo model in Caenorhabditis elegans for the conserved RNA ligase RtcB and show that RtcB ligates the xbp-1 mRNA during the IRE-1 branch of the unfolded protein response. Without RtcB, protein stress results in the accumulation of unligated xbp-1 mRNA fragments, defects in the unfolded protein response, and decreased lifespan. RtcB also ligates endogenous pre-tRNA halves, and RtcB mutants have defects in growth and lifespan that can be bypassed by expression of pre-spliced tRNAs. In addition, animals that lack RtcB have defects that are independent of tRNA maturation and the unfolded protein response. Thus, RNA ligation by RtcB is required for the function of multiple endogenous target RNAs including both xbp-1 and tRNAs. RtcB is uniquely capable of performing these ligation functions, and RNA ligation by RtcB mediates multiple essential processes in vivo.

Coevolution of RtcB and Archease created a multiple-turnover RNA ligase

“…Likewise, RtcB is required for tRNA splicing in humans (Popow et al 2011). Moreover, RtcB activity is also required for XBP1 splicing during the unfolded protein response in metazoa Kosmaczewski et al 2014;Lu et al 2014). Attesting to the importance of Archease activating RtcB in mammals, a decrease in the concentration of Archease has been shown to impair both tRNA splicing and XBP1 splicing Popow et al 2014).…”

“…RtcB is an essential enzyme for the ligation of tRNAs in metazoa (Popow et al 2011), and possibly archaea Sarmiento et al 2013), upon intron removal by the tRNA splicing endonuclease (Abelson et al 1998;Popow et al 2012). RtcB is also essential for the ligation of XBP1 exons in metazoa upon intron removal by IRE1, which initiates the unfolded protein response during endoplasmic reticulum stress Kosmaczewski et al 2014;Lu et al 2014). RtcB-catalyzed RNA ligation proceeds through three nucleotidyl transfer steps, with 2 ′ ,3 ′ -cyclic phosphate termini being hydrolyzed to 3 ′ -p termini in a step that precedes 3 ′ -p activation with GMP Chakravarty and Shuman 2012;Chakravarty et al 2012).…”

Physiological/pathological ramifications of transcription factors in the unfolded protein response

“…In yeast cells (Saccharomyces cerevisiae), activated Ire1p cleaves the unspliced HAC1 mRNA at two RNA stem-loops to excise an intervening 252-base intron, and then the tRNA ligase Trl1p joins the two exons followed by removal of the junctional 2 ′ phosphate in the second step by 2 ′ phosphotransferase Tpt1p, generating the spliced form of HAC1 mRNA (Sidrauski et al 1996;Sidrauski and Walter 1997;Schwer et al 2004). Similarly, in metazoans, IRE1α first removes a 23-nt (Caenorhabditis elegans and Drosophila melanogaster) or 26-nt (mammals) intron from the unspliced XBP1 mRNA (Tirasophon et al 1998;Shen et al 2001;Yoshida et al 2001;Calfon et al 2002), and the proximally located tRNA ligase RTCB joins the two cleaved XBP1 exons to generate a mature mRNA to produce the spliced form of XBP1 (Kosmaczewski et al 2014;Lu et al 2014). XBP1 mRNA appears to be the only substrate for IRE1α for splicing, as sophisticated searches for other substrates have failed (Bai et al 2014).…”

Metazoan tRNA introns generate stable circular RNAs in vivo

“…2B). In metazoa, ligation of the two exonic tRNA halves is thought to be carried out by a complex that contains RtcB-like proteins (Popow et al 2011(Popow et al , 2014Kosmaczewski et al 2014). To determine whether RtcB is also important for formation of tricRNAs, we carried out RNA interference (RNAi) in vivo.…”