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  • Review Article
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Giant proteins that move DNA: bullies of the genomic playground

Nature Reviews Molecular Cell Biology volume 7, pages 580–588 (2006)Cite this article

Key Points

  • Five major ideas regarding the highly specialized proteins that move DNA are discussed in this review.

  • Proteins move DNA. A protein can be thought of as moving on DNA, or alternatively, DNA can be moving past the protein. Depending on what moves, the consequences are dramatically different. Movement of DNA within the cell has to be regulated and must be accurate with respect to cell division. This is one of a number of occasions that require the DNA to be moved, not the protein.

  • DNA movers are large. Many of the DNA-moving proteins have a total molecular mass of over a million Daltons, whereas more passive DNA-binding proteins are uniformly small. These enzymes are large because they need large surfaces to multimerize and interact with DNA, and because they are often composites of multiple activities.

  • Enzymes use energy to enforce reaction directionality. Nucleotide binding and release is often as important in luring enzymes into catalytically proficient states as ATP hydrolysis itself. DNA motors such as topoisomerases often employ the binding of ATP to produce specific structural changes in the enzyme that ensure reaction directionality. Topoisomerases use energy to reduce topological entanglements to sub-equilibrium levels.

  • Directed stochasticity. Counter-intuitively, DNA-moving enzymes often act stochastically rather than in a deterministic fashion. Their action at a given instant is not always in the direction of the overall process. The DNA translocase FtsK, DNA-replication forks and microtubule polymerization all have this property. The ability to 'capture' molecules that have successfully reached their precise location following movement presumably allowed this simple and robust strategy to arise several times throughout the course of evolution.

  • Moving DNA has topological consequences. A common but unexpected feature of all DNA translocases is that motion of the DNA leads to changes in its topology. They produce changes in twist (which is convertible to writhe), ahead of and behind the protein, that require removal by topoisomerases. Only recently have single-molecule biophysical techniques allowed these important changes to be measured.

Abstract

As genetic material DNA is wonderful, but as a macromolecule it is unruly, voluminous and fragile. Without the action of DNA replicases, topoisomerases, helicases, translocases and recombinases, the genome would collapse into a topologically entangled random coil that would be useless to the cell. We discuss the organization, movement and energetics of these proteins that are crucial to the preservation of a molecule that has such beautiful biological but challenging physical properties.

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Figure 1: Conformational changes during type II topoisomerase action.
Figure 2: DNA translocation by FtsK is globally unidirectional but locally bidirectional.
Figure 3: Stochastic initiation and movement of the replication fork.

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Acknowledgements

The authors would like to dedicate this work to our friend and colleague N. Cozzarelli, who passed away during the completion of this review. We acknowledge N. Crisona for critical reading of this manuscript. Work in our laboratories was supported by the National Institutes of Health (N.R.C. and T.V.), Ruth Kirschtein awards (J.S. and G.C.) and the Human Frontiers Science Organization (M.N.).

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  1. Department of Molecular and Cell Biology, 16 Barker Hall, University of California at Berkeley, Berkeley, 94720-3204, California, USA

    Nicholas R. Cozzarelli, Gregory J. Cost, Marcelo Nöllmann, Thierry Viard & James E. Stray

  2. in memoriam,

    Nicholas R. Cozzarelli

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Glossary

DNA motors

DNA-binding enzymes that use energy to move a segment of DNA processively from one point to another or to track along DNA.

Septum

The protein ring at the mid-point of a bacterial cell that demarcates the site of future cell division.

Replisome

A multiprotein complex that is involved in DNA replication.

Ground state/transition state

The most stable/least stable (lowest-energy/highest-energy) state of a chemical reaction.

B-form DNA

A right-handed double-helical conformation of DNA that is the most common form seen in solution.

Decatenase/catenase

An enzyme that removes/adds catenanes.

Endergonic reaction

A reaction that consumes or traps energy.

Exergonic reaction

A reaction that produces or releases energy.

Catenane

A topologically linked circular molecule.

dif

A 28-nucleotide sequence near the terminus of DNA replication in E. coli that is the recognition site for the XerC and XerD recombinases.

AAA+ family of ATPases

(ATPases with associated activities). A large family of ATP hydrolases that is typified by a highly conserved catalytic motif. The members of the family greatly vary in both form and function.

Kinetochore

A large multiprotein complex that assembles onto the centromere of the chromosome and links the chromosome to the microtubules of the mitotic spindle.

Protomer

Any of the subunits of which an oligomeric protein is built up.

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Cozzarelli, N., Cost, G., Nöllmann, M. et al. Giant proteins that move DNA: bullies of the genomic playground. Nat Rev Mol Cell Biol 7, 580–588 (2006). https://doi.org/10.1038/nrm1982

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