1. Volume 21, Issue 5, Pages 595-604 (March 2006)
DNA Repeat Rearrangements Mediated by DnaK-Dependent Replication Fork Repair 
Stephen J. Goldfless, Aviv Segal Morag, Kurt A. Belisle, Vincent A. Sutera, Susan T. Lovett 
Molecular Cell 
Volume 21, Issue 5, Pages (March 2006)
DOI: /j.molcel
Copyright © 2006 Elsevier Inc. Terms and Conditions

2. Figure 1 Proposed Template-Switching Repair Mechanism
(A) An arrested replication fork with loaded DnaB helicase (hexagon) and DNA polymerase III complex bound to processivity clamps (ovals).
(B) DnaK may be required to dislodge the polymerase to allow the unwinding of nascent strands, while the DnaB fork helicase remains loaded. Unwinding may be aided by a DNA helicase-clamp interaction.
(C) Nascent strands pair, forming a Holliday junction, concomitant with a template switch to allow replication of the gapped region. If the switch occurs in a region with directly repeated sequences, mispairing at this step can generate repeat deletion or expansion.
(D) Processing of Holliday junction to yield a crossover between sister chromosomes. Alternative processing (data not shown) can yield noncrossover products.
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2
Misalignment Mechanisms for Rearrangements and Genetic Assays for Rearrangements
(A–D) Simple slippage of the nascent strand (gray lines) on its template (black lines) in the context of directly repeated sequences (gray or black boxes) can yield (A) deletion of direct repeats or (B) expansion of direct repeats. Crossfork misalignment of nascent strands (gray lines) causes a template-switch reaction that can give rise to (C) deletion or (D) expansion of direct repeats. Parental strands (black lines) may also pair, but for simplicity of presentation, this pairing is not shown in these schemes. Because of the potential to generate Holliday junctions (see Figure 1), crossfork slippage can be accompanied by sister chromosome crossing over; simple slippage cannot.
(E) Genetic assays used to detect rearrangements between repeated sequences. Plasmid pSTL55 (and its chromosomal integrant in STL695 derivatives) detects deletion between 787 bp tandem repeats (shown as boxes) to yield an intact tetracycline-resistance tetA gene; plasmid pSTL57 similarly detects deletion between tandem 101 bp repeats. Plasmid pEXPBR detects expansion of two 787 bp repeats to a triplication, yielding an intact tetA gene. Plasmids pMB302 and pMB303 assay deletion between 101 bp tetA repeats interspersed by inverted repeats.
Molecular Cell  , DOI: ( /j.molcel )
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4. Figure 3 Survival Phenotypes of dnaK Mutant Derivatives
MG1655 (wild-type), closed circles; STL7155 (dnaK::EZ-Tn5), closed squares; STL8517 (dnaKΔ), closed triangles; STL8709 (dnaK306), closed diamonds; STL3817 (recA::cat), open circles; STL7155 (dnaK::Tn5)/pBAD33, open squares; STL7155 (dnaK::Tn5)/pBAD33-dnaKJ+, open triangles; and STL8747 (dnaK306 recA::cat), open diamonds.
(A–C) Fractional survival to various doses of UV (A), HU (B), and AZT (C). Error bars represent standard deviations.
(D) Colony morphology on LB medium after overnight growth at 30°C of the MG1655 derivatives MG1655 (wild-type), STL7180 (recA::cat), STL8709 (dnaK306), and STL8747 (dnak306 recA::cat).
(E) Genetic epistasis of dnaK and dnaX. UV survival of MG1655 (wild-type), closed circles; STL8709 (dnaK306), closed diamonds; STL8786 (dnaX2016), open inverted triangles; and STL9645 (dnaK306 dnaX2016), closed inverted triangles.
Molecular Cell  , DOI: ( /j.molcel )
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5. Figure 4 Expression of SOS-Induced Genes, recA, and dinB
Luciferase activity was measured in the indicated strain with the use of luciferase gene fusions (Van Dyk et al., 2001), with (gray bars) and without (black bars) 45 min prior treatment with AZT at 1 μg/ml. Arbitrary expression values are derived from the scintillation counts per minute divided by total colony-forming units of the culture. (Note that different scales for luciferase units are used for the two assays because the recA promoter is stronger than that for dinB.) The data represent the mean and standard deviation of three to four experiments.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions