The cyclic phosphodiesterase CNP and RNA cyclase RtcA fine-tune noncanonical XBP1 splicing during ER stress

J Biol Chem. 2018 Dec 14;293(50):19365-19376. doi: 10.1074/jbc.RA118.004872. Epub 2018 Oct 24.


The activity of X box-binding protein 1 (XBP1), a master transcriptional regulator of endoplasmic reticulum (ER) homeostasis and the unfolded protein response (UPR), is controlled by a two-step noncanonical splicing reaction in the cytoplasm. The first step of nuclease cleavage by inositol-requiring enzyme 1 (IRE1), a protein kinase/endoribonuclease, is conserved in all eukaryotic cells. The second step of RNA ligation differs biochemically among species. In yeast, tRNA ligase 1 (Trl1) and tRNA 2'-phosphotransferase 1 (Tpt1) act through a 5'-PO4/3'-OH pathway. In metazoans, RNA 2',3'-cyclic phosphate and 5'-OH ligase (RtcB) ligate XBP1 exons via a 3'-PO4/5'-OH reaction. Although RtcB has been identified as the primary RNA ligase, evidence suggests that yeast-like ligase components may also operate in mammals. In this study, using mouse and human cell lines along with in vitro splicing assays, we investigated whether these components contribute to XBP1 splicing during ER stress. We found that the mammalian 2'-phosphotransferase Trpt1 does not contribute to XBP1 splicing even in the absence of RtcB. Instead, we found that 2',3'-cyclic nucleotide phosphodiesterase (CNP) suppresses RtcB-mediated XBP1 splicing by hydrolyzing 2',3'-cyclic phosphate into 2'-phosphate on the cleaved exon termini. By contrast, RNA 3'-terminal cyclase (RtcA), which converts 2'-phosphate back to 2',3'-cyclic phosphate, facilitated XBP1 splicing by increasing the number of compatible RNA termini for RtcB. Taken together, our results provide evidence that CNP and RtcA fine-tune XBP1 output during ER stress.

Keywords: CNP; RNA processing; RNA splicing; RtcA; RtcB; Trpt1; X-box binding protein 1 (XBP1); gene regulation; signaling; stress response; unfolded protein response (UPR).

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase / metabolism*
  • Animals
  • Endoplasmic Reticulum Stress / genetics*
  • HEK293 Cells
  • Humans
  • Ligases / metabolism*
  • Mice
  • RNA Splicing*
  • Tumor Protein, Translationally-Controlled 1
  • X-Box Binding Protein 1 / genetics*


  • TPT1 protein, human
  • Tpt1 protein, mouse
  • Tumor Protein, Translationally-Controlled 1
  • X-Box Binding Protein 1
  • XBP1 protein, human
  • 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase
  • CNP protein, human
  • Cnp protein, mouse
  • Ligases
  • RNA 3'-terminal phosphate cyclase