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, 165 (5), 1171-1181

Active Yeast Telomerase Shares Subunits With Ribonucleoproteins RNase P and RNase MRP

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Active Yeast Telomerase Shares Subunits With Ribonucleoproteins RNase P and RNase MRP

Bruno Lemieux et al. Cell.

Abstract

Telomerase is the ribonucleoprotein enzyme that replenishes telomeric DNA and maintains genome integrity. Minimally, telomerase activity requires a templating RNA and a catalytic protein. Additional proteins are required for activity on telomeres in vivo. Here, we report that the Pop1, Pop6, and Pop7 proteins, known components of RNase P and RNase MRP, bind to yeast telomerase RNA and are essential constituents of the telomerase holoenzyme. Pop1/Pop6/Pop7 binding is specific and involves an RNA domain highly similar to a protein-binding domain in the RNAs of RNase P/MRP. The results also show that Pop1/Pop6/Pop7 function to maintain the essential components Est1 and Est2 on the RNA in vivo. Consistently, addition of Pop1 allows for telomerase activity reconstitution with wild-type telomerase RNA in vitro. Thus, the same chaperoning module has allowed the evolution of functionally and, remarkably, structurally distinct RNPs, telomerase, and RNases P/MRP from unrelated progenitor RNAs.

Figures

Figure 1
Figure 1. Mass spectrometry of endogenously expressed telomerase RNPs identifies the Pop1/Pop6/Pop7 proteins as part of active telomerase complexes
(A) Fractions from indicated steps during the purification as analyzed by western blotting. Blots were probed with anti Myc-antibodies (top) or anti-ProA antibodies (bottom). IN: input protein extract; FT: proteins in flow through; W1 BE: proteins retained on beads after the first wash; Fin BE: final proteins on the beads fraction that was used for mass spectrometry. The TLC1 alleles used are indicated on top. (B) Left: Telomerase activity assays from cells expressing a ProA-Est2 protein and enriched with IgG as positive control. Right: Final telomerase activity on the IgG beads using the extracts from the cells as in panel A. +/− RNase: sample treatment with RNase A. 0+P32: 32P end-labeled substrate oligo. Band labeled with a star is a background band migrating at the +3 position. (C) Combined results from three independent mass spectrometry determinations. Proteins identified are listed in order of the sum of peak-intensities (right column). The total number of unique peptides for each protein and the total protein coverage are indicated. Only proteins that were detected exclusively in the MS2-tagged Tlc1 fraction were considered and the top eight proteins are listed. For a more extensive list, see Figure S1A.
Figure 2
Figure 2. Binding of the Pop1/Pop6/Pop7 proteins to the Tlc1 RNA is specific
(A) Northern analysis of immunoprecipitations using IgG covered beads with extracts from strains expressing the indicated TAP-tagged proteins. For the HA3-Pop1, anti-HA antibodies were used. The blots were hybridized with probes specific for the Tlc1 RNA and the Nme1 RNA at the same time. Ctrl RNAs on left: total RNAs from a wt strain or a strain that carried a tlc1Δ allele. IN: RNA from the input fraction IP: RNA from the immunoprecipitates; FT: RNA extracted from the unbound fraction. (B) Northern analysis as performed in panel (A). (C) Telomerase activity enrichment using a tagged Pop1, Pop6, or Pop7 protein. Top: antibodies used for immunoprecipitations with extracts derived from strains harboring the indicated tagged proteins. ProA-Est2 serves as positive control. Note that direct and indirect anti-HA refers to whether the anti-HA antibody was directly coupled to magnetic beads or whether antibody was first mixed with the slurry and then immunopurified with Protein A/G coupled magnetic beads. For the HA-tagged Pop1 protein, the latter technique appears more efficient in telomerase recuperation. Labeling as in Figure 1B. See also Figure S1B.
Figure 3
Figure 3. The CS2a/TeSS domain is a P3-like domain in Tlc1
(A) Schematic representation of the TeSS structure at the distal end of stem IVc of Tlc1 (left), the P3 domain of Nme1 RNase MRP RNA (middle) and the P3 domain of the Rpr1 RNase P RNA (right). Dark blue shading: identical nucleotides, light blue: purines and pyrimidines are conserved. Purple blue line on left of Tlc1: CS2a (Conserved Sequence element 2a; Gunisova et al., 2009). Dark green line on Nme1 RNA: nucleotides protected by Pop6/Pop7 binding (Perederina et al., 2007). For more details, see Figure S2A). (B) Telomere length analyses in strains harboring the indicated TLC1 alleles. TLC1: wild type; Δ: tlc1Δ; ΔL: tlc1-ΔL allele that lacks the TeSS/P3 domain (see Figure S4); P3NME1: tlc1::P3NME1, the TeSS/P3 domain in the Tlc1 RNA was replaced with the one from the Nme1 RNA; P3RPR1; tlc1::P3RPR1, the TeSS/P3 domain in Tlc1 was replaced with the one from the Rpr1 RNA. +: Strain carried a wt TLC1 gene on a URA3 plasmid. Black wedges indicate outgrowth of strains after loss of the plasmid borne TLC1 gene; last lane reflects growth for 110 generations. Schematic structures on top are color coded as the nucleotides in panel (A). (C) Growth assays of cells that contain the indicated NME1 alleles: nme1Δ, complete deletion of NME1; ΔP3: nme1-ΔP3 allele that lacks the P3 domain; nme1::P3TLC1 the NME1 P3 domain was replaced with the TLC1 TeSS/P3 domain. Bottom plate: all strains contained a wt NME1 gene on a plasmid with the URA3 marker. Top plate: growth of cells after loss of the URA3, NME1 containing plasmid. Schematic structures and color coding as in panel A.
Figure 4
Figure 4. A cold sensitive allele of the NME1 P3 domain confers cold-sensitive telomere shortening
Telomere length analyses in strains harboring the indicated TLC1 alleles. Lanes 1–4: TLC1; lanes 5–8: tlc1Δ; lane 9–12: tlc1-ΔL; lanes 13–16: tlc1-ΔL; lanes 17–20: tlc1-P3NME1; lanes 21–24: tlc1-P3nme1-11. Schematics of stem IVc structures and color coding as in Figure 3 (see also Figure S4A). +: Strain carried a wt TLC1 gene on a URA3 plasmid. Black triangles: growth of cells after loss of the wt TLC1 gene at 30°C for 30 and 110 generations. Lanes with the blue star: strains were grown at 18°C for 110 generations. The red/blue bar at bottom indicates the temperatures the respective strain was grown at.
Figure 5
Figure 5. Binding characteristics of the Pop6/Pop7 heterodimer to the Tlc1 P3 domain in vitro and in vivo
(A) Binding curves and apparent Kds of the Pop6/Pop7 heterodimer binding to indicated RNA oligonucleotides (see predicted structures, complete binding curve and gel assays in Figure S3). (B) Northern blot analysis of co-immunoprecipitated RNAs using IgG beads and extracts of strains that harbored TAP-tagged Pop7, a wt Tlc1 RNA and a 400 nt longer MS2-tagged Tlc1 RNA. The latter either contained a wt stem IVc, lanes 3–5; lacks the most distal stem-loop, MS2-tlc1-ΔS: lanes 6–8; or lacks the TeSS/P3 completely, MS2-tlc1-ΔL, lanes 9–11. IN: input (2.5%); IP: immunoprecipitates (10%); FT: flowthrough (2.5%). (C) Western blot of input (left) and immunoprecipitates (right) from strains harboring a Myc13-tagged Sme1 protein and Pop7-TAP. TCL1 alleles as indicated. See Figure S4A for predicted structures of the stem IVc in these mutated RNAs.
Figure 6
Figure 6. The Tlc1 TeSS/P3 domain is required for telomerase RNP integrity and function in vivo and in vitro
(A) Western blots of input (left) and IPs (right) with extracts from strains harboring a HA3-tagged Sme1 protein and in which the Est1 as well as Est2 proteins carried a Myc12-tag. TLC1 alleles as indicated. Below, Northern blot of RNA extracted from equal amounts of the inputs (left) or IPs (right) as used for the Western, and which was hybridized to a TLC1-specific probe. (B) Telomerase activity assays with in vitro reconstituted RNPs using the Mini-T RNA (Zappulla et al., 2005). ProA-Est2 levels after the RRL reaction are indicated below. Recombinant rPop6/Pop7 heterodimer and/or rPop1 proteins were added as indicated. After the RRL assay, telomerase was enriched using IgG beads and activity was assayed as in Figure 1. Bar graph depicts quantified telomerase activities standardized to the one obtained without Pop protein addition (lane 2; * p < 0.05 as determined in an unpaired t-test with Welch’s correction). (C) Telomerase activity assays with in vitro reconstituted RNPs using a full-length wt Tlc1 RNA. Indications as in (B).
Figure 7
Figure 7. Model for core structure of the active yeast telomerase RNP
(A) Telomerase activity assays with in vitro reconstituted RNPs using the Mini-T RNA, increasing amounts of Pop1 with or without Pop6/Pop7 addition as indicated. Final Pop1 concentrations are 0 (lanes 3, 7); 0.11 μM (lanes 4, 8); 0.33 μM lanes 5, 9) and 1 μM lanes 6, 10). Quantification of relative telomerase activities is indicated on the right. No additional protein addition (lane 3) was set as 1; data are averages from two experiments. (B) Binding of the Pop6/Pop7 and Pop1 proteins are modeled on top of the newly identified TLC1 P3 domain of the yeast telomerase RNA. The presence of the Tlc1 P3 domain provides a protein binding platform that keeps the essential Est1 and Est2 proteins on the active RNP. Note that physical interactions between the Pop-proteins and Est1 or Est2 as well as the placement of Est3 in the model are hypothetical.

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