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Structures of the human CST-Polα–primase complex bound to telomere templates

Abstract

The mammalian DNA polymerase-α–primase (Polα–primase) complex is essential for DNA metabolism, providing the de novo RNA–DNA primer for several DNA replication pathways1,2,3,4 such as lagging-strand synthesis and telomere C-strand fill-in. The physical mechanism underlying how Polα–primase, alone or in partnership with accessory proteins, performs its complicated multistep primer synthesis function is unknown. Here we show that CST, a single-stranded DNA-binding accessory protein complex for Polα–primase, physically organizes the enzyme for efficient primer synthesis. Cryogenic electron microscopy structures of the CST-Polα–primase preinitiation complex (PIC) bound to various types of telomere overhang reveal that template-bound CST partitions the DNA and RNA catalytic centres of Polα–primase into two separate domains and effectively arranges them in RNA–DNA synthesis order. The architecture of the PIC provides a single solution for the multiple structural requirements for the synthesis of RNA–DNA primers by Polα–primase. Several insights into the template-binding specificity of CST, template requirement for assembly of the CST-Polα–primase PIC and activation are also revealed in this study.

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Fig. 1: The architecture of the human CST-Polα–primase PIC bound to a telomere overhang.
Fig. 2: The molecular and structural basis for the binding preference of CST to telomeric sequences.
Fig. 3: CST arranges the catalytic centres of Polα–primase in RNA–DNA synthesis order along the template.
Fig. 4: PRIM2C is flexibly poised to perform de novo RNA primer synthesis and facilitate primer handover.
Fig. 5: The human primase structure that is poised for RNA primer synthesis.

Data availability

The described cryo-EM maps and coordinate files have been deposited in the Electron Microscopy Data Bank and the Protein Data Bank (PDB) under the accession codes EMD-27097 (co-complex–3×TEL-consensus); EMD-27099 (co-complex–3×TEL-local-refined-merged); EMD-27104, PDB ID 8D0B (co-complex–4×TEL-local-refined-merged and consensus maps and model); EMD-27107, PDB ID 8D0K (co-complex–4×TEL–PRIM2C-advanced PIC-local-refined-merged and consensus maps and model); and EMD-27109 (co-complex–6×TEL-local-refined-merged and consensus). The coordinates were assembled and built from individual predicted models from the AlphaFold Protein Structure Database https://alphafold.ebi.ac.uk/.

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Acknowledgements

We thank T. Tahirov and A. Baranovskiy from the University of Nebraska Medical Center for initial discussion and suggestions in setting up our experiments. We thank T. Cech and A. Zaug from the University of Colorado Boulder for help, discussion and suggestions. We also thank our departmental colleagues S. Butcher and J. Kimble for helpful input, discussion and critical reading of the manuscript. We also thank the members of the laboratory of C.L. for helpful discussions and suggestions. This research was, in part, supported by the Cryo-EM Research Center in the Department of Biochemistry at the University of Wisconsin–Madison and the National Cancer Institute’s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract 75N91019D00024. Support for this research was provided to C.L. by the National Institutes of Health, the National Institute of General Medical Sciences (R00GM131023) and the University of Wisconsin–Madison, Office of the Vice-Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation and the Department of Biochemistry.

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Authors and Affiliations

Authors

Contributions

Q.H. and C.L. designed the expression constructs for recombinant protein production, with support from B.L.L., and Q.H. and X.L. performed insect cell culture and baculovirus production for insect cell infection. Q.H. expressed and purified the recombinant human protein complexes. Q.H., B.L.C. and C.L. conducted the negative-stain EM data collection and sample screening. Q.H. and C.L. prepared the cryo-EM samples for data collection. C.L. processed and analysed the cryo-EM datasets with support from Q.H. C.L. and Q.H. performed model building and refinement. C.L. and X.L. performed the enzyme assays, and C.L., X.L. and Q.H. analysed the data. Q.H., X.L., S.A. and B.L.C. performed the electrophoresis mobility shift assays, and Q.H., S.A., X.L. and B.L.C. analysed the data. C.L. directed the project and designed the experiments with input from Q.H., X.L., B.L.C. and S.A. C.L. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Ci Ji Lim.

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The authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1 Recombinant human CST and pol-α/primase purification and their biochemical characterization assays.

(a) Tandem affinity tags purification of CST and pol-α/primase complexes from baculovirus-infected insect cells. CST heterotrimeric complex was purified by first using Ni-NTA beads to pull down 6xHis-STN1 and 6xHis-TEN1 and then using anti-FLAG beads to pull-down 3xFLAG-CTC1. Pol-α/primase 4-subunit complex was purified by first using Ni-NTA beads to pull down 6xHis-PRIM1, 6xHis-PRIM2, and 6xHis-POLA2 and then using Strep beads to pull-down Strep-POLA1. FT: flowthrough. Trident (GeneTex) high-range prestained protein marker was used in both coomassie-stained denaturing protein gels. The results are reproducible across multiple independent experiments (n > 5). (b) Pull-down assay to characterize direct protein-protein interactions between CST and full-length or truncated (ΔPOLA11-337) pol-α/primase (ΔN-Pol-α/primase). Strep beads were used with pol-α/primase as bait and CST as prey. All input lanes are loaded as 10% of the total sample. Molecular weight markers are annotated for size reference. The pull-down results are reproducible across multiple independent experiments (n = 3). (c) Predicted RNA-DNA primers that are made by pol-α/primase using the repetitive telomeric DNA template in ATP-rich NTP reaction conditions. Primer product sizes are calculated assuming the polymerase reaches the end of the template. (d) Fold-stimulation analysis of direct enzyme assays done at predicted RNA-DNA primer product level (see Fig. 1c). CST does not stimulate pol-α/primase with the 3xTEL template, whether measured at the individual primer product level or total activity (see Fig. 1d). CST can stimulate pol-α/primase using the 6xTEL template. Data are plotted using bars for mean values and error bars for standard deviation as calculated from three independent experiments (n = 3). Data points from each experiment are represented by circle-filled markers in each corresponding bar. The dashed line marked fold-stimulation of one (no stimulation) and values were calculated by dividing the band intensity counts over the corresponding counts from the band and lane without CST added.

Extended Data Fig. 2 Negative-stain electron microscopy 2D classification analysis of CST-pol-α/primase co-complex bound to different telomeric ssDNA template lengths and structures.

(a) Top ten (by distribution) class averages of CST-pol-α/primase preincubated with various lengths of telomeric single-stranded DNA, from 2.5 to 6 repeats of TTAGGG, and structures (ssDNA versus ss/dsDNA). 3xTEL-FB is a DNA template that has a 15 bp hairpin structure at the 5’ end of the GG(TTAGGG)2TTAG overhang. (b) Top ten (by distribution) 2D class averages of each apo-state CST, pol-α/primase, and CST-pol-α/primase co-complex. No new PIC structure was observed in the absence of a template. Instead, individual CST or pol-α/primase 2D class averages were seen in the co-complex analysis. CST-like and pol-α/primase class averages are pointed out by color-coded arrows for visual comparison.

Extended Data Fig. 3 3xTEL, 4xTEL-FB, and 6xTEL co-complexes share the same overall PIC structure.

(a) Comparison of the three co-complexes consensus cryo-EM maps at two different map thresholds. (b) Fourier-shell correlation (FSC) values of the 3xTEL PIC cryo-EM map aligned against the 4xTEL-FB map or 6xTEL map. The FSC values are reported at the level of 0.143.

Extended Data Fig. 4 Pol-α/primase conformation comparison in its apo-state vs. its preinitiation-state.

Pol-α/primase architecture changes from a compact shape to a segregated form upon forming the preinitiation complex (PIC) with a template-bound CST. The APO and PIC structures are depicted as ribbon cartoons. The CST complex and template are hidden in the PIC state to better demonstrate the segregated architecture of the PIC structure – separated into polymerase and primase domains. The lobe boundaries are loosely defined by the dashed lines – black for the polymerase domain and grey for the primase domain. The POLA1 DNA catalytic center is highlighted in orange to illustrate its accessibility upon forming the PIC. POLA1CAT thumb subdomain and PRIM2C domain are not illustrated in the PIC structure because of their flexibility (see main text).

Extended Data Fig. 5 CST and Pol-α/primase interactions.

(a) Overview of TEN1 interactions with primase domain. TEN1 is depicted as surface representation while the primase subunits are drawn as ribbons. (b) TEN1 and STN1N interface sits the PRIM184-101 loop. (c) TEN1 also made contacts with the alpha-helix nine (α9) of the PRIM2N domain. (d) Two hydrogen bonds were identified between TEN1 and POLA2 subunit; TEN1E98 to POLA2R217 and TEN1Q47 to POLA2E277. (e) The loop between residues 547-556 of POLA1 sits on the CTC1OB-G. The POLA1 loop is depicted with heteroatom-coloured sidechains. (f) The template bound by CTC1 forms hydrogen bonds with POLA1 charged residues Q554, N652, and K672. (g) STN1C interacts with POLA1 using negatively charged residues E352 and S355. On the opposite surface, POLA1 uses the positively charged residues H627, H658, and K661. (h, i) The surfaces where POLA1 and STN1C contact has complementary charged residues. In panel h, the POLA1 STN1C-interacting surface, encircled by a white dashed circle, is positively charged. The colour key for the coulombic electrostatic potential is shown at the bottom right of the panel. In panel i, for STN1C, its POLA1-interacting surface, circle by a white dashed circle, is negatively charged. The white dashed circles represent the area of contact for the two protein subunits.

Extended Data Fig. 6 Comparisons of PRIM2N conformation in enzyme apo and preinitiation states and POLA1EXO-CAT domain conformation in the enzyme apo, preinitiation and elongation state.

(a) The PRIM2N structure from our PIC model was compared against the pol-α/primase model in the APO-state (PDB: 5EXR). The PRIM2N small and large subdomains were the same for both enzymatic states but the domain relative position had rotated by about 40°. The structures were aligned using the small subdomain to illustrate the large domain shift. (b) Top-down view of the POLA1EXO-CAT domain at various enzymatic states; apo (APO), preinitiation (PIC), and DNA elongation (ELO). To note, the APO- and ELO-state structures were obtained from either pol-α/primase (PDB: 5EXR) or POLA1 catalytic domain (PDB: 4QCL) alone. The PIC-state was derived from the CST-pol-α/primase co-complex structure. The RNA-DNA primer-template structure of the ELO-state is depicted as a space-filled model. The side-view perspective of each enzyme state is also shown for comparison.

Extended Data Fig. 7 Analysis of PIC-template interactions.

(a) Model of the 15 nt telomeric sequence built into template cryo-EM density (shown as semi-transparent grey coloured volume). The model is depicted as an atomic model that is color-coded T=blue, A=red, and G=green. The modelled sequence is 5’- TAGGGTTAGGGTTAG – 3’ (15mer-TTAG). (b) Model-to-map cross-correlation (CC) analysis reported at per residue level and chain average. The experimental binding affinities of CST to these templates are provided. The template 15mer-TAGG and 15mer-AGGG sequences are 5’- AGGGTTAGGGTTAGG – 3’ and 5’- GGGTTAGGGTTAGGG – 3’ respectively. (c) Independent experiments and quantification for Fig. 2b. See Supplementary Table 1 for template sequences. (d) Overview of protein-DNA interactions involved in template binding. (e, f) CTC1OB-F interactions with the template at the binding site 1. (g) CTC1OB-G residues binding to the template at binding site two are shown. (h) POLA1 residues binding to the template at binding site 2 are shown. (i) STN1 W89 base stacks with A14 of the template. This is supported by T13-T14 base stacking. (j) Other protein-DNA interactions between STN1N and template at binding site 3. STN1 R139 hydrogen bonds with T13 phosphate backbone and STN1 Y141 base stacks with G15 aromatic base. (k) The 15 nt DNA template model is depicted as a deep pink atomic model. Sites 1 and 2 are positively charged while site 3 is more neutral. Site 1 DNA-binding residues are mostly made from CTC1OB-F, site 2 residues are from CTC1OB-G and POLA1, and site 3 residues are from the STN1N domain. The electrostatic potential colour key is in units of kcal/(mol·e) at 298 K.

Extended Data Fig. 8 CST-pol-α/primase PIC structure is incompatible with CST decamer formation at early oligomerization states.

(a) Dimension comparison of the PIC model to the CST decamer model (ten copies of CST; PDB: 6W6W). (b) The PIC primase domain is not sterically hindered by the CST inverted dimer and thus could exist. However, its polymerase domain directly clashes with CST dimer formation. (c) The PIC primase and polymerase domains clash with CST tetramer formation. As in panel b, the polymerase domain clashes with the dimer formation, while the primase domain is now in the way of the fourth CST in the CST tetramer model. Subunits are coloured as in Fig. 1 for all panels.

Extended Data Fig. 9 Polymerase domain swivels on top of the template-bound CST.

(a) Three-dimensional (3D) variable analysis (3DVA) principal component analysis revealed a mode that showed the polymerase domain rotating about on the top of the template-bound CST. The first and last frames of the PCA mode are shown here as pink and navy blue cryo-EM maps. The cryo-EM maps are filtered to a resolution of 8 Å. The polymerase domain swivelling motion is seemly controlled by the STN1C domain and rotation angle restrained by the STN1 linker. (b) The corresponding components in A depicted on the PIC atomic model. CTC1 is represented as surface and coloured light grey. The rest of the PIC are drawn as ribbons. The color scheme follows Fig. 1.

Extended Data Fig. 10 Cryo-EM heterogeneity analysis reveals template-bound human primase structure at an advanced preinitiation state.

(a) The 4xTEL-FB PIC structure was masked with a PRIM1-PRIM2C for particle subtraction and 3D classification to isolate a subset of particles that allowed higher-resolution 3D reconstruction of the PRIM2C domain. An eight classes 3D classification step without image alignment was used to sieve out a conformation (~13.8%) that has an extra EM density in front of the PRIM1 subunit. This subtracted particles subset (32,550 particles) was reverted to their original images before subjecting to 3D refinement to obtain a 4.3 Å cryo-EM map. The resolved PRIM2C domain density is circled in green dashed lines. (b) Two crystal structure variants of the PRIM2C domain are docked into the cryo-EM density that was resolved in Fig. 5 and panel a. The all-helical variant (PDB: 3Q36) is a better fit than the β-sheet-containing version (PDB: 3L9Q), as can be seen in the region pointed out by the black arrow. (c) PRIM1 and PRIM2C have minimal contacts except for two loop regions; PRIM1192-200 and PRIM2376-385. (d) PRIM1 and PRIM2 interactions with the template region into the primase crevice. (e) The five additional template residues were built based on the resolved primase density. The last three nucleotides are annotated. (f) The PRIM1 and PRIM2C domains form a crevice that the template sits in for RNA primer synthesis. The crevice has the PRIM1 RNA catalytic center facing the template. (g) The 3’ end of the extended 20 nt template model in the PIC structure connects seamlessly with the template model in the previously solved RNA-DNA primer-template-bound PRIM2C crystal structure (PDB: 5F0Q).

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Supplementary Figs. 1–10 and Tables 1 and 2.

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Supplementary Video 1

3DVA analysis of the polymerase domain swivelling on top of a template-bound CST in a PIC structure.

Supplementary Video 2

3DVA analysis of the PRIM2(C) domain sampling the space in front of PRIM1 and POLA1 and the template.

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He, Q., Lin, X., Chavez, B.L. et al. Structures of the human CST-Polα–primase complex bound to telomere templates. Nature 608, 826–832 (2022). https://doi.org/10.1038/s41586-022-05040-1

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