A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus

Abstract

Emerging evidence suggests that Argonaute (Ago)/Piwi proteins have diverse functions in the nucleus and cytoplasm, but the molecular mechanisms employed in the nucleus remain poorly defined. The Tetrahymena thermophila Ago/Piwi protein Twi12 is essential for growth and functions in the nucleus. Twi12-bound small RNAs (sRNAs) are 3' tRNA fragments that contain modified bases and thus are attenuated for base pairing to targets. We show that Twi12 assembles an unexpected complex with the nuclear exonuclease Xrn2. Twi12 functions to stabilize and localize Xrn2, as well as to stimulate its exonuclease activity. Twi12 function depends on sRNA binding, which is required for its nuclear import. Depletion of Twi12 or Xrn2 induces a cellular ribosomal RNA processing defect known to result from limiting Xrn2 activity in other organisms. Our findings suggest a role for an Ago/Piwi protein and 3' tRNA fragments in nuclear RNA metabolism.

Figure 1. Full-length Twi12 binds tRNA fragments

(A) Schematic of Twi12 compared to Twi12^S, which is truncated by 17 amino acids at the N-terminus. See Figure S1 for further description of strains. (B) RNA co-purified with ZZF-Twi12 or ZZ-Twi12^S, resolved by urea-PAGE and stained by SYBR Gold. Total RNA is from the same cells, which express ZZF-Twi12 or ZZ-Twi12^S from the uninduced MTT1 promoter and do not express endogenous Twi12. (C) Library composition of sequenced 18–22 nt sRNAs co-purified with ZZF-Twi12 expressed from the endogenous TWI12 promoter, mapped allowing for one internal mismatch and a 3' overhang of C, CC, or CCA.

Figure 2. Twi12-bound sRNAs are derived from the 3' ends of mature tRNAs

(A) Annotated reads in each category analyzed for the fraction that map perfectly (black), with one mismatch (gray), or with a 3' overhang of C, CC, or CCA (blue and light blue, see key). Reads annotated as mRNA and rRNA are most likely misannotated. (B) Plot showing number of reads with 5' ends at each tRNA location: 5' end, D stem-loop, anticodon stem-loop (A), variable stem-loop (V), or TΨC stem-loop (T). (C) Two-dimensional thin layer chromatographic analysis of ³²P post-labeled 5' monophosphate nucleosides. The diagram at right shows the positions of the conserved tRNA base modifications that are indicated in the chromatographs. The solid black line indicates the Twi12-bound fragment. Asterisks indicate modified base positions in the Twi12-bound fragment that are pseudouridine (Ψ) or 1-methyl adenosine (m¹A).

Figure 3. Twi12 interacts with Xrn2 and Tan1

(A) SDS-PAGE and silver staining after two-step IP of ZZF-Twi12 expressed from the endogenous locus. The first step was IgG IP and TEV protease elution, and the second step was anti-FLAG IP and urea elution. (B) Table of ZZF-Twi12-associated proteins identified by mass spectrometry. See also Figures S2A and S2B. (C) SDS-PAGE and silver staining after one-step IP of the proteins identified by mass spectrometry. Filled circles indicate the tagged protein in each lane, which runs as two bands (ZZF-tagged and F-tagged) because of proteolytic clipping between the tag segments. Labels at right indicate the migration positions of untagged proteins, and small Xs mark Xrn2 N-terminal proteolysis fragments. Note that tagged Tan1 does not silver stain strongly. See also Figures S2C and S2D. (D) Illustrated model of TXT with bound sRNA. Asterisks on the line representing sRNA indicate base modifications. Direct interaction of Tan1 with Twi12 is not established.

Figure 4. TXT is a nuclear complex with 5' monophosphate-dependent exonuclease activity

(A) Indirect IF for each subunit in TXT. (B) Nuclease activity assay on TXT purified by each subunit. Top panel: silver stained proteins after one-step IP. Middle panel: RNA after in vitro incubation with TXT. Note that N-terminally tagged Xrn2 is catalytically inactive. Bottom panel: sRNAs associated with each population of TXT in vivo. See Figure S3 for analysis of a potential Tan1 activity.

Figure 5. Twi12 nuclear localization is dependent on sRNA binding

(A) SDS-PAGE and silver staining after one-step IP of ZZF-Twi12 wild-type and variants expressed from the uninduced MTT1 promoter (top), with SYBR Gold-staining of associated sRNA (bottom). (B) Indirect IF for ZZF-Twi12 wild-type and variants expressed from the uninduced MTT1 promoter. See also Figure S4.

Figure 6. Depletion of Twi12 or Xrn2 induces a pre-rRNA processing defect

(A) Twi12 or Xrn2 depletion was achieved by cadmium removal from cells with the genotypes schematized at top (see also Figure S5). Bottom: western blot probed with anti-FLAG and anti-tubulin, with loading normalized for cell equivalents of whole-cell extract. (B) Top: schematic of the Tetrahymena rRNA RNAP I transcript. Gray lines show positions of probes, and the 26S rRNA intron is also shown. Bottom: Northern blot analysis of total RNA samples normalized by cell equivalents. Blots were made from two gels loaded with the same RNA samples; both blots were probed for RPL21 mRNA as a control for equivalent loading. The asterisk indicates full-length or near full-length pre-rRNA transcript. Numbers below each panel indicate signal intensity normalized to that of wild-type cells. (C) SYTO RNA select staining of Twi12 iKD and Xrn2 iKD cells cultured with and without cadmium. Note that both RNA and DNA are stained by SYTO RNA select in these paraformaldehyde-fixed cells.

Figure 7. Xrn2 requires Twi12 for accumulation, nuclear localization, and activity

(A) Genetic strategy for generation of the cell line in which Xrn2 is tagged in the Twi12 iKD background. (B) Western blot probed with IgG or anti-FLAG, with loading normalized for cell equivalents of whole-cell extract. (C) SDS-PAGE and silver staining after one-step IgG IP of Xrn2-ZZ from cell extracts. (D) Indirect IF for Xrn2-ZZ in cells with Twi12 expressed (+Cd²⁺) or depleted (−Cd²⁺). Note that there is some cell-to-cell variability in transgene expression level. (E) Nuclease activity. Top panel: silver stained samples after purification and depletion as indicated. Bottom panel: RNA after in vitro incubation with each purified sample.