1. Structural Biology and Molecular Biophysics
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Single-molecule view of coordination in a multi-functional DNA polymerase

  1. Raymond F Pauszek III
  2. Rajan Lamichhane
  3. Arishma Rajkarnikar Singh
  4. David P Millar  Is a corresponding author
  1. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, United States
Research Article
Cite this article as: eLife 2021;10:e62046 doi: 10.7554/eLife.62046
9 figures, 10 tables and 1 additional file

Figures

Activities of Pol I and three-dimensional structures of Pol I homologs.

(A) Processes catalyzed by Pol I during lagging strand DNA replication or base excision repair. A growing primer strand is extended through repeated cycles of nucleotide incorporation, resulting in displacement of a downstream strand (RNA in the case of Okazaki fragment maturation or DNA in the case of base excision repair). The resulting substrate rearranges to a double flap structure that is cleaved by the 5’ nuclease activity of Pol I (site indicated by a half arrow head). The final ligation step is performed by a DNA ligase (not shown). (B) Crystal structure of the Pol I homolog Taq polymerase with DNA primer/template bound in the pol domain (PDB ID: 1TAU). The polymerase core is shown in gray and the 5’ nuc domain is shown in light blue. (C) Crystal structure of human FEN1 bound to a DNA substrate (PDB: 3Q8M). In both B and C, the DNA strands are colored as in A and the green and red arrows denote the approximate locations of the sites for donor (scheme 2) or acceptor (scheme 1) labeling, respectively.

DNA substrates used in this study.

(A) Substrate containing a 5’ flap on the downstream strand (designated downstream flap DNA). (B) Substrate containing the same 5’ flap as in A, plus a single unpaired base at the primer 3’ terminus (designated double flap DNA). Because of the base sequences of the strands (Appendix 1), the structures shown in A and B are ‘locked in’. (C) Substrate that can exist as a mixture of the structures shown in A and B (designated mixed flap DNA). (D) Substrates containing a nick (n = 0) or gaps of various size (n = 1–4). (E). Primer/template substrate. (F) Schematic illustration of donor (green) and acceptor (red) labeling sites for the first FRET scheme. Pol I is depicted in cartoon form, with the core colored grey and the 5' nuc domain colored blue. (G) Schematic illustration of donor (yellow) and acceptor (blue) labeling sites for the second FRET scheme.

Figure 3 with 4 supplements
Probing the location of DNA substrates within Pol I.

(A) Schematic representation of the donor (green, attached to primer strand) and acceptor (magenta, attached to thumb region of Pol I) labeling sites. Pol I is depicted in cartoon form, with the core colored gray and the 5’ nuc domain colored blue. (B) Representative smFRET trajectory (blue) and donor (green) and acceptor (magenta) emission trajectories, for Pol I interacting with mixed flap substrate. The bold line is the idealized state path determined from Hidden Markov modeling. (C) Composite FRET efficiency histograms for states P and N, compiled from n individual FRET trajectories (n value indicated in each plot), for various combinations of DNA substrate and protein. The proteins, from top to bottom, are WT Pol I, Pol I L361A, and KF L361A. The corresponding populations of states P and N are indicated. (D) Transition density plots for Pol I interacting with flap-containing DNA substrates, compiled from a total of n transitions. From left to right: double flap DNA, mixed flap DNA and downstream flap DNA. (E) Rate constants for intramolecular transfer of DNA substrates from pol domain to 5’ nuc domain (P→N) or from 5’ nuc domain to pol domain (N→P).

Figure 3—figure supplement 1
Additional examples of smFRET trajectories (blue) and corresponding donor intensity (green) and acceptor intensity (red).

The bold lines are idealized state paths from Hidden Markov modeling.

Figure 3—figure supplement 2
Interaction of Pol I with mismatched primer/template.

(A) Schematic illustration of mismatched primer/template. (B) FRET efficiency histogram for Pol I interacting with mismatched primer/template. (C) FRET efficiency histogram for Pol I containing L361A mutation interacting with mismatched primer/template. The fractional populations of states E and P are indicated in each case.

Figure 3—figure supplement 3
Histogram of emission intensities resulting from direct excitation of A594 in Pol I bound to downstream flap DNA, compiled from 102 individual emission trajectories.

The single peak centered at ∼350 a.u. indicates that only one enzyme molecule binds to the DNA. The peak at ∼0 a.u. corresponds to periods during which Pol I is not bound to the DNA.

Figure 3—figure supplement 4
Dwell time histograms for overall decay of state P (left column) or state N (right column) for Pol I interacting with flap-containing DNA substrates, compiled from a total of n transitions.

The solid lines are best fits to a single exponential function, with the rate constants indicated.

Figure 4 with 2 supplements
Interaction of Pol I with primer/template DNA or DNA substrates containing a nick or gap.

(A) Representative smFRET trajectories for DNA substrates interacting with Pol I, as indicated. Schematic representations of DNA substrates are shown in Figure 2. Bold lines are idealized state paths determined from Hidden Markov modeling. (B) Composite FRET efficiency histograms for states P and N compiled from n individual FRET trajectories, for various DNA substrates interacting with Pol I, as indicated. The corresponding populations of states P and N are indicated. (C) Transition density plots for Pol I interacting with various DNA substrates compiled from a total of n transitions, as indicated. (D) Rate constants for intramolecular transfer of various DNA substrates between pol domain and 5’ nuc domain (P→N, grey) or between 5’ nuc domain and pol domain (N→P, blue).

Figure 4—figure supplement 1
Histograms and TDPs of Pol I L361A and KF interacting with 1nt gap DNA.

Composite FRET efficiency histograms (left) and transition density plots (right) for Pol I L361A (top panels) and KF (bottom panels) interacting with 1nt gap substrate. The numbers of trajectories or transitions used to compile each plot are indicated.

Figure 4—figure supplement 2
Dwell time histograms for overall decay of state P (left column) or state N (right column) for Pol I interacting with nick- or gap-containing DNA substrates, compiled from a total of n transitions.

The solid lines are best fits to a single-exponential function, with the rate constants indicated.

Probing the location of the 5’ nuc domain within Pol I bound to flap substrates.

(A) Schematic representation of donor (yellow, attached to 5’ nuc domain) and acceptor (cyan, attached to downstream template strand) labeling sites. (B) Representative set of donor, acceptor and FRET trajectories for mixed flap DNA substrate. The bold lines are idealized state paths from Hidden Markov modeling. (C) FRET efficiency histograms compiled from n individual FRET trajectories. (D) Transition density plots compiled from a total of n transitions. Since the FRET efficiency is not defined during periods when Pol I is not bound to DNA, the FRET efficiency is set to −0.2. The quadrant enclosed by the dotted lines corresponds to periods during which Pol I is bound to DNA.

Location of the 5’ nuc domain within Pol I bound to primer/template substrate.

(A) Schematic representation of donor (yellow) and acceptor (cyan) labeling sites. (B) Representative set of donor, acceptor and FRET trajectories. (C) FRET efficiency histograms compiled from n individual FRET trajectories. (D) Transition density plot compiled from a total of n transitions. Same presentation as Figure 5D.

Possible configurations of Pol I-DNA complexes.

Complex P’: in the absence of a nearby downstream strand, the primer 3’ terminus resides in the pol domain within the enzyme core (grey) and the 5’ nuc domain (blue) is extended away from the core. The donor and acceptor probes for the first labeling scheme are green and magenta, respectively, while the donor and acceptor for the second labeling scheme are yellow and blue. The FRET efficiencies for the first and second labeling schemes are denoted E1 and E2, respectively. Complex P: The primer 3’ terminus resides in the pol domain and the 5’ nuc domain is located in proximity to a nearby downstream strand. Complex N: The 5’ nuc domain is docked with the downstream strand and the DNA primer 3’ terminus resides within the same domain.

Appendix 2—figure 1
PAGE analysis of Pol I expression and purification steps.

(M = size marker; FT = flow-through).

Author response image 1

Tables

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (Escherichia coli)CJ803Yale coli genetic stock center
Recombinant DNApXS67Yale coli genetic stock center
Commercial assay or kitQ5 site-directed mutagenesis kitNew England Biolabs#E0554
Quik Change kitAgilent200523
Chemical compoundAlexa Fluor 488 NHS esterThermo FisherA20000
Alexa Fluor 488 C5 maleimideThermo FisherA10254
Alexa Fluor 594 NHS esterThermo FisherA20004
Alexa Fluor 594 C5 maleimideThermo FisherA10256
Software, algorithmscikit_learnotherpublic domain
Software, algorithmSciPyotherpublic domain
Appendix 1—table 1
Sequences of DNA oligonucleotides used to construct substrates for FRET scheme 1.
SubstrateOligo nameSequence
Double flap17e5'-TCGCAGCCGYCAATATg
T2b3'-BT10-AGCGTCGGCAGTTATAGATATAGCTTCGGAACAC −5'
D18c_2taCTATATCGAAGCCTTGTG −3'
Mixed flap17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D18b_2taGTATATCGAAGCCTTGTG −3'
Downstream flap17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D18c_2tacTATATCGAAGCCTTGTG −3'
Nick17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D17bTATATCGAAGCCTTGTG −3'
1nt gap17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D16bATATCGAAGCCTTGTG −3'
2nt gap17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D15bTATCGAAGCCTTGTG −3'
3nt gap17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D14bATCGAAGCCTTGTG −3'
4nt gap17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
D13bTCGAAGCCTTGTG −3'
Primer/template17e5'-TCGCAGCCGYCAATATG
T1b3'-BT10-AGCGTCGGCAGTTATACATATAGCTTCGGAACAC −5'
Primer/template-17e5'-TCGCAGCCGYCAATATg
mismatchT2b3'-BT10-AGCGTCGGCAGTTATAGATATAGCTTCGGAACAC −5'
Appendix 1—table 2
Sequences of DNA oligonucleotides used to construct substrates for FRET scheme 2.
SubstrateOligo nameSequence
Double flapP18mmt5'-ACTTGAGAGCCGTATGAg
T33Y3'-BT10-TGAACTCTCGGCATACTGGTAAYGGTAGCGTGC −5'
D16ttCCATTACCATCGCACG −3'
Mixed flapP185'-ACTTGAGAGCCGTATGAC
T33Y3'-BT10-TGAACTCTCGGCATACTGGTAAYGGTAGCGTGC −5'
D16ttCCATTACCATCGCACG −3'
Downstream flapP185'-ACTTGAGAGCCGTATGAC
T33Y3'-BT10-TGAACTCTCGGCATACTGGTAAYGGTAGCGTGC −5'
D16mmtttgCATTACCATCGCACG −3'
Primer/templateP15'-ACTTGAGAGCCGTATG
T33Y3'-BT10-TGAACTCTCGGCATACTGGTAAYGGTAGCGTGC −5'
Appendix 3—table 1
Binding of Pol I to flap-containing DNA substrates.
SubstratefBKd (nM)
Double flap0.28 ± 0.0313 ± 2
Mixed flap0.27 ± 0.0414 ± 3
Downstream flap0.22 ± 0.0318 ± 3
Appendix 3—table 2
Statistical frequencies of state-to-state transitions for Pol I interacting with flap-containing substrates.
Transition frequencies
SubstratefPNfPUfNPfNU
Double flap0.6 ± 0.10.4 ± 0.10.4 ± 0.10.6 ± 0.1
Mixed flap0.4 ± 0.10.6 ± 0.10.4 ± 0.10.6 ± 0.1
Downstream flap0.34 ± 0.040.66 ± 0.040.4 ± 0.10.6 ± 0.1
Appendix 3—table 3
Rate constants for state-to-state transitions for Pol I interacting with flap-containing substrates.
Rate constants (s-1)
SubstratekPNkPUkNPkNU
Double flap1.2 ± 0.10.6 ± 0.20.56 ± 0.051.0 ± 0.2
Mixed flap0.58 ± 0.040.8 ± 0.20.8 ± 0.11.3 ± 0.3
Downstream flap0.34 ± 0.020.7 ± 0.11.6 ± 0.12.1 ± 0.4
Appendix 3—table 4
Statistical frequencies of state-to-state transitions for Pol I interacting with nick- or gap-containing substrates.
Transition frequencies
SubstratefPNfPUfNPfNU
Nick0.4 ± 0.10.6 ± 0.10.5 ± 0.10.5 ± 0.1
1nt gap0.64 ± 0.040.36 ± 0.040.67 ± 0.040.33 ± 0.04
2nt gap0.6 ± 0.10.4 ± 0.10.7 ± 0.10.3 ± 0.1
3nt gap0.6 ± 0.10.4 ± 0.10.66 ± 0.040.34 ± 0.04
4nt gap0.54 ± 0.050.46 ± 0.050.7 ± 0.10.3 ± 0.1
Appendix 3—table 5
Rate constants for state-to-state transitions for Pol I interacting with nick- or gap-containing substrates.
Rate constants (/s)
SubstratekPNkPUkNPkNU
Nick0.47 ± 0.020.6 ± 0.11.5 ± 0.11.7 ± 0.3
1nt gap0.52 ± 0.020.30 ± 0.041.6 ± 0.10.8 ± 0.1
2nt gap0.34 ± 0.020.23 ± 0.041.3 ± 0.10.6 ± 0.1
3nt gap0.32 ± 0.020.23 ± 0.041.14 ± 0.050.6 ± 0.1
4nt gap0.20 ± 0.020.17 ± 0.031.4 ± 0.10.6 ± 0.2
Appendix 3—table 6
Binding of Pol I to various DNA substrates.
SubstratefBKd (nM)
Nick0.20 ± 0.0220 ± 3
1nt gap0.39 ± 0.028 ± 1
2nt gap0.47 ± 0.046 ± 1
3nt gap0.52 ± 0.055 ± 1
4nt gap0.56 ± 0.044 ± 1
primer/template0.27 ± 0.0214 ± 2
Appendix 4—table 1
Steady-state fluorescence controls.
Labeled macromoleculeLabelLigandNormalized intensity a,bAnisotropy a
Double flapA488none1.00.05 ± 0.01
Pol I0.940.21 ± 0.05
Primer/templateA488none1.00.05 ± 0.01
Pol I1.20.22 ± 0.01
Pol IA594none1.00.32 ± 0.02
double flap1.20.34 ± 0.03
primer/template1.10.34 ± 0.03
  1. a total emission intensity normalized to the value for the free macromolecule b A488 data obtained with excitation at 495 nm, A594 with excitation at 590 nm

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