1. Structural Biology and Molecular Biophysics
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Hexameric helicase G40P unwinds DNA in single base pair steps

  1. Michael Schlierf  Is a corresponding author
  2. Ganggang Wang
  3. Xiaojiang S Chen
  4. Taekjip Ha  Is a corresponding author
  1. University of Illinois at Urbana-Champaign, United States
  2. Technische Universität Dresden, Germany
  3. University of Southern California, United States
  4. Howard Hughes Medical Institute, United States
  5. Johns Hopkins University, United States
Research Article
Cite this article as: eLife 2019;8:e42001 doi: 10.7554/eLife.42001
5 figures, 1 table and 3 additional files

Figures

Figure 1 with 3 supplements
G40P unwinds DNA in one base pair steps und slips backwards.

(a) Schematic illustration of the smFRET unwinding assay. After loading to the substrate G40P unwinds the dsDNA (containing between 0 and 3 consecutive GC base pairs after 10 AT base pairs) and thereby gradually separates the donor fluorophore from the acceptor fluorophore. Complete unwinding results in donor strand leaving from the surface. (b) Typical unwinding trace of G40P. At tinject the protein solution containing Mg.ATP is injected. The unwinding initiation time tinit depends on the protein concentration and is measured from the moment of protein solution injection until unwinding starts. The unwinding time tunw is determined from the moment of FRET efficiency decrease until donor strand leaving. (c) Typical FRET efficiency unwinding traces of G40P on an all AT substrate base pair. The scale bar indicates 1 s. (d) Typical FRET efficiency unwinding traces of G40P with one GC base pair. The helicase briefly stalls at a characteristic FRET efficiency or slips after stalling and unwinds in a second attempt. (e) Typical FRET efficiency unwinding traces of G40P on the substrate with two consecutive GC base pairs. The helicase stalls eventually at two distinct FRET efficiencies (see arrows). (f) Typical FRET efficiency unwinding traces of G40P on the substrate with three consecutive GC base pairs. The helicase rarely unwinds three consecutive GC base pairs completely (top trace). Most traces show unwinding attempts and stalls at distinct FRET efficiency levels (bottom trace). (g-i) FRET efficiency distribution of stall levels of the one GC (blue), two GC (black) and three GC base pair (red) substrate. A (multipeak) fit with Gaussians revealed one peak at EFRET = 0.52 ± 0.04 for 1GC, two peaks at EFRET = 0.53 ± 0.04 and at EFRET = 0.39 ± 0.04 (two dashed lines) for 2GC and three peaks at EFRET = 0.52 ± 0.04, EFRET = 0.38 ± 0.04 and at EFRET = 0.27 ± 0.04 (three dashed lines) for 3GC. (j) Average FRET efficiencies with stalls after 4AT, 7AT, 10AT and 13AT base pairs (black symbols) in comparison with peak positions of stalls induced by 1GC, 2GC and 3GC base pairs (blue symbols).

https://doi.org/10.7554/eLife.42001.003
Figure 1—figure supplement 1
Choice of substrate, data selection, Michaelis-Menten kinetics and kinetic step size of G40P.

(a) Opposite fluorophore attachment to the forked dsDNA substrate yield a wide FRET change range during unwinding. A typical trace is shown on the right-hand side. (b) Labeling the non-tracking strand with the donor and acceptor fluorophores relies for the FRET efficiency change on the shorter persistence length of ssDNA compared to dsDNA. Both fluorophores do not have to pass through the central pore of the helicase and yield identical average unwinding times. However, the FRET efficiency change signal is much less clear (right). (c) Selection criteria for traces to be included in the analysis. Typical unwinding trace of G40P. At tinject the protein solution together with Mg.ATP is injected. The unwinding initiation time tinit depends on the protein concentration and is measured from the moment of protein solution injection until unwinding starts. smFRET traces were tested for acceptor survival by means of direct excitation with a 633 nm laser to exclude acceptor bleaching events from analysis. During the unwinding assay, only donor molecules were excited with a 532 nm laser. In the illustrated trace, unwinding was observed at t ≈ 22 s, the acceptor test was performed at t ≈ 96–97.5 s. (d) The unwinding initiation rate (1/tinit) is shown as a function of G40P hexamer concentration and can be fitted linearly (errors are standard deviation). Inset: The unwinding time is independent of the protein concentration within error. (e) Percentage of initial high FRET traces with successful unwinding events without anti-digoxigenin and with anti-digoxigenin at the 5’ tail of the forked duplex (*** denotes p<0.001). Inset: Schematic illustration of the digoxigenin-modified substrate (square at the 5’ tail) blocked by anti-digoxigenin (yellow). (f) Typical FRET efficiency unwinding traces at [ATP]=3 mM, 1 mM, 250 µM, 150 µM, 100 µM and 75 µM. The unwinding appears smooth and the unwinding time increased with decreasing ATP concentration. (g) Typical FRET efficiency traces at [ATP]=250 µM and with increasing [ADP]=0 mM, 0.5 mM and 1 mM. The effect of ADP as competitive inhibitor can be directly observed with increasing unwinding times. (h) Semi-logarithmic plot of the average unwinding rate (1/tunw) as a function of ATP concentration (errors are standard deviation). The average unwinding rate at different ATP concentrations was determined without ADP (red squares), with 0.5 mM ADP (green circles), with 1 mM ADP (blue triangles) and 5 mM Pi (black rhomboids). The solid lines are fits to the data using Michaelis-Menten equation. The red dashed is a fit to the 0 mM ADP data with the Hill-equation. (i) Unwinding time distribution of the AT substrate by (G40P)6 at 1 mM ATP. Fit is a Gamma distribution with a stepping rate k = 21.9 s−1 and a number of steps n = 10.1. (j) Unwinding time distribution of the AT substrate by (G40P)6 at 250 µM ATP. The fit is a Gamma distribution with a stepping rate k = 16.4 s−1 and a number of steps n = 10.1.

https://doi.org/10.7554/eLife.42001.004
Figure 1—figure supplement 2
GC induced stalls and unwinding length-FRET calibration.

(a) Stall lifetime distribution of G40P stalls on the 1GC substrate. A single exponential fit yields a characteristic lifetime of 79 ± 5 ms. (b) Fraction of all traces with protein activity with complete unwinding on different substrates (AT, 1GC, 2GC, 3GC) and at 21°C and 33°C, respectively (n.s. denotes not significant, *p<0.05, ***p<0.001). (c) Sketch of the intrinsic calibration constructs with x AT base pairs followed by 40-x GC base pairs. Due to its exquisite sequence sensitivity G40P stalls at the GC base pairs. (d) Stall FRET level histograms for four different substrates: 4AT, 7AT, 10AT and 13AT. The Histograms were evaluated with Gaussian fits. The leakage of donor fluorescence to the acceptor channel was determined to give an apparent EFRET = 0.11 ± 0.02. (e) through (h) Sample traces of calibration substrates 4AT, 7AT, 10AT and 13AT, respectively, with the analyzed stall level indicated by arrows.

https://doi.org/10.7554/eLife.42001.005
Figure 1—figure supplement 3
Unwinding traces of the AT DNA substrate by (G40P)6 in presence of 1 mM ATP and 10 mM CaCl2 instead of 10 mM MgCl2.

Traces are offset for clarity. Black lines and grey shade represent the stall FRET efficiency levels of the consecutive GC base pairs at position 11, 12 and 13 for reference of consecutive FRET levels.

https://doi.org/10.7554/eLife.42001.006
Expected stalling positions induced by GC base pairs.

Stalling sites for 1GC (a), 2GC (b) or 3GC (c) substrate. (left) Assuming a one nt step size of G40P, the FRET efficiency distribution of GC induced breaks would show 1, 2 or 3 peaks for 1, 2 or three consecutive GC base pairs. (right) Assuming a two nt step size of G40P, the FRET efficiency distribution of GC induced breaks would show 2, 3 or 4 peaks for 1, 2 or three consecutive GC base pairs, due to the phase of the first stepping event. GC base pairs in bold lines, helicase as blue ring structure. Number below the DNA substrates indicate the breaking position of the helicase relative to the first GC base pair.

https://doi.org/10.7554/eLife.42001.007
Figure 3 with 1 supplement
Primase DnaG prevents helicase slippage.

(a) FRET efficiency traces of the G40P-DnaG complex on the 3GC substrate. Traces with successful unwinding showed no slippage events. (b) Fraction of all traces with protein activity with complete unwinding on different substrates (AT, 1GC, 2GC, 3GC) and at different enzyme conditions (G40P, G40p+DnaG) (n.s. denotes not significant, *p<0.05, ***p<0.001). (c) FRET efficiency traces of G40P unwinding the AT substrate with slippage events marked by stars before the actual unwinding events marked by the arrow at [ATP]=250 µM, 150 µM and 100 µM. (d) Semi-logarithmic plot of the average number of slippage events per total number of unwinding traces at different ATP concentrations. Addition of DnaG reduces the average number of slippage events before successful unwinding by a factor ≈ 2.5. Errors were estimated by bootstrapping analysis.

https://doi.org/10.7554/eLife.42001.008
Figure 3—figure supplement 1
Unwinding traces of the 3GC DNA substrate by (G40P)6 in presence of DnaG.

Top panels: Donor (green) and acceptor (red) time traces. Bottom panels: FRET efficiency time traces.

https://doi.org/10.7554/eLife.42001.009
Figure 4 with 1 supplement
ATPγS poisoning of G40P unwinding reactions reveals sequential ATP hydrolysis.

(a) Typical FRET efficiency traces at [ATP]=1 mM in the left panel and [ATP]+[ATPγS]=0.975 mM+0.025 mM in the right panel. The unwinding traces with 2.5% ATPγS show a clear stalling event (highlighted in green) that is absent at 0% ATPγS. (b) Lifetime distribution of the first stall during unwinding at several ATPγS percentages. A single exponential fit is used to evaluate the characteristic lifetime. (c) The stall lifetime evaluated from single exponential fits as a function of ATPγS poisoning percentage. Within error the characteristic lifetime is independent of ATPγS concentration. The linear fit is to guide the eye. (d) Fraction of unwinding traces with a stall event during FRET decrease between 0% and 1% ATPγS. A linear increase is expected if a single ATPγS binding event stalls the helicase. (e) Stall FRET efficiency distribution of ATPγS induced stalls.

https://doi.org/10.7554/eLife.42001.010
Figure 4—figure supplement 1
ATPγS affinity to G40P and induced stalls during unwinding.

(a) ATPase activity of G40P tested with EnzChek Phosphate detection kit (Invitrogen). After addition of ATP and depletion of free phosphates, G40P was added to the solution (20 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2). We observed without any ssDNA present in solution a significant ATPase activity. Addition of ssDNA to the solution increased the ATPase activity of G40P by a factor of two. (b) The ATPase activity of G40P without ssDNA was successfully suppressed by exchanging MgCl2 to MnCl2. After addition of ssDNA, G40P showed approximately 50% of the ATPase activity as in case (a). (c) Normalized fluorescence as function of the competitor. Preformed mant-ADP G40P complexes were titrated with ATP (green circles) and ATPγS (red circles). In both cases the fluorescence signal decreased rapidly. The data was evaluated using eq 1. (d) Stall lifetime of non-ATPγS induced stalling events at saturating ATP conditions. The typical lifetime was determined to be t0 = 0.05 ± 0.01 s, significantly shorter than ATPγS induced stalls with t ≈ 0.44 s. (e) Fraction of unwinding traces with a stall event during FRET decrease between 0% and 10% ATPγS. A linear increase is expected if a single ATPγS binding event stalls the helicase. At higher ATPγS concentrations the fraction of traces with a stalling event saturate. Inset: Fitted Michaelis-Menten model assuming ATPγS as an inhibitor (dashed line). (f) Average unwinding rate of G40P of the AT substrate as a function of ATPγS fraction (total nucleotide concentration was 1 mM, ATPγS concentration was increased from 0 to 100 µM).

https://doi.org/10.7554/eLife.42001.011
How translocation leads to unwinding.

Schematic illustrations of dsDNA unwinding by G40P of AT base pairs (a), at a GC base pair induced break (b), at sub-saturating ATP concentrations (c), in complex with the primase DnaG (d), and in case of ATPγS induced breaks (e). For detailed description see text.

https://doi.org/10.7554/eLife.42001.012

Tables

Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional
information
Genetic reagent (SPP1)G40PDOI: 10.1038/nsmb1356
Genetic reagent (B.subtilis)DnaGDOI: 10.1038/nsmb1356
Software, algorithmMATLABMathworks Matlab Version
R2009, R2010, R2018
home written scripts for
data analysis. Available
in Supplementary file 2.
Commercial assay or kitEnzChek Phosphate
Assay Kit (Invitrogen)
EnzChek Phosphate Assay Kit
(Invitrogen; now from
ThermoFisher)
Cat #. E6646ATPase activity Kit
Sequence-based reagentDNA Oligos
(Supplementary file 1 - Table S5)
DNA Oligos were ordered from IDTDNA oligos
Othermant-ADPmant-ADP (Invitrogen;
now ThermoFisher)
Cat #. M12416fluorescent nucleotide

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Due to their large size (~200Gb total), raw video data files are available upon request.

Additional files

Supplementary file 1

Table S1 to S5 reporting number of events, fractions and DNA oligo sequences.

https://doi.org/10.7554/eLife.42001.013
Supplementary file 2

MATLAB scripts for data analysis.

https://cdn.elifesciences.org/articles/42001/elife-42001-supp2-v2.m
Transparent reporting form
https://doi.org/10.7554/eLife.42001.014

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