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Review
. 2009 Feb;37(3):738-48.
doi: 10.1093/nar/gkn937. Epub 2008 Nov 28.

The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing

Joseph E Deweese  1 , Neil Osheroff
Affiliations
Review

The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing

Joseph E Deweese et al. Nucleic Acids Res. 2009 Feb.

Abstract

Topoisomerase II is an essential enzyme that is required for virtually every process that requires movement of DNA within the nucleus or the opening of the double helix. This enzyme helps to regulate DNA under- and overwinding and removes knots and tangles from the genetic material. In order to carry out its critical physiological functions, topoisomerase II generates transient double-stranded breaks in DNA. Consequently, while necessary for cell survival, the enzyme also has the capacity to fragment the genome. The DNA cleavage/ligation reaction of topoisomerase II is the target for some of the most successful anticancer drugs currently in clinical use. However, this same reaction also is believed to trigger chromosomal translocations that are associated with specific types of leukemia. This article will familiarize the reader with the DNA cleavage/ligation reaction of topoisomerase II and other aspects of its catalytic cycle. In addition, it will discuss the interaction of the enzyme with anticancer drugs and the mechanisms by which these agents increase levels of topoisomerase II-generated DNA strand breaks. Finally, it will describe dietary and environmental agents that enhance DNA cleavage mediated by the enzyme.

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Figures

Figure 1.
Figure 1.
Nuclear processes induce changes in DNA topology. DNA replication is used as an example. Although chromosomal DNA is globally underwound in all cells, the movement of DNA tracking systems generates positive supercoils. As shown in (A) chromosomal DNA ends are tethered to membranes or the chromosome scaffold (represented by the red spheres) and are unable to rotate. Therefore, the linear movement of tracking systems (such as the replication machinery represented by the yellow bars) through the immobilized double helix compresses the turns into a shorter segment of the genetic material and induces acute overwinding (i.e. positive supercoiling) ahead of the fork (B). In addition, the compensatory underwinding (i.e. negative supercoiling) behind the replication machinery allows some of the torsional stress that accumulates in the prereplicated DNA to be translated to the newly replicated daughter molecules in the form of precatenanes (C). If these precatenanes are not resolved, they ultimately lead to the formation of intertwined (i.e. tangled) duplex daughter chromosomes. Adapted from ref. 10.
Figure 2.
Figure 2.
Double-stranded DNA cleavage mediated by topoisomerase II. Scissile bonds are located four bases apart on opposite strands of the double helix. During cleavage, the active site tyrosine residue of each topoisomerase II protomer subunit becomes covalently linked to the newly generated 5′-terminal phosphate moiety on each strand. This covalent linkage preserves the energy of the sugar-phosphate DNA backbone. The newly generated 3′-hydroxyl group interacts with topoisomerase II in a noncovalent fashion. Ligation represents the reverse of this process and leaves the DNA product chemically unchanged from the initial substrate.
Figure 3.
Figure 3.
Mechanism of DNA cleavage and ligation mediated by topoisomerase II. The type II enzyme utilizes a two-metal ion mechanism similar to that utilized by primases and polymerases (34,70,71,74–77,155,156). Amino acids that are postulated to interact with the metal ions in the active site of topoisomerase IIα and topoisomerase IIβ are indicated. One of the metal ions (shown at left) makes a critical interaction with the 3′-bridging atom of the scissile phosphate (bond shown in red), which most likely is needed to stabilize the leaving 3′-oxygen (shown in red). A second metal ion (shown at right) is required for DNA scission and may stabilize the DNA transition state and/or help deprotonate the active site tyrosine (Y805 in topoisomerase IIα and Y821 in topoisomerase IIβ). Cleavage is initiated when a general base deprotonates the active site tyrosine hydroxyl, allowing the oxyanion to attack the scissile phosphate. The base has not been identified but is believed to be a conserved histidine residue. Ligation is initiated when a general acid extracts the hydrogen from the 3′-terminal hydroxyl group. The acid may be a water molecule or an unidentified amino acid in the active site of topoisomerase II. Figure adapted from Noble and Maxwell (73).
Figure 4.
Figure 4.
Topoisomerase II is an essential but genotoxic enzyme. The formation of topoisomerase II–DNA cleavage complexes is required for the enzyme to perform its critical cellular functions. If the level of topoisomerase II–DNA cleavage complexes falls too low (left arrow), cells are not able to untangle daughter chromosomes and ultimately die of mitotic failure. If the level of cleavage complexes becomes too high (right arrow) the actions of DNA tracking systems can convert these transient complexes to permanent double-stranded breaks. The resulting DNA breaks, as well as the inhibition of essential DNA processes, initiate recombination/repair pathways and generate chromosome translocations and other DNA aberrations. If the strand breaks overwhelm the cell, they can trigger apoptosis. This is the basis for the actions of several widely prescribed anticancer drugs. If the concentration of topoisomerase-mediated DNA strand breaks is too low to overwhelm the cell, mutations or chromosomal aberrations may be present in surviving populations. In some cases, exposure to topoisomerase II poisons has been associated with the formation of specific types of leukemia that involve the MLL (mixed lineage leukemia) gene at chromosome band 11q23 or the chromosome 15;17 translocation that joins the PML (promyelocytic leukemia) and RARA (retinoic acid receptor α) genes (lower right arrow).
Figure 5.
Figure 5.
Topoisomerase II anticancer drugs. Structures of selected topoisomerase II-targeted anticancer drugs are shown.
Figure 6.
Figure 6.
Dietary, environmental and DNA-based topoisomerase II poisons. Abbreviations used are epigallocatechin gallate (EGCG), N-acetyl-p-benzoquinone imine (NAPQI) and 2-(4-chloro-phenyl)-[1,4]benzoquinone (4′Cl-2,5pQ).
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