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nvolved in controlling DNA topology during multiple processes of DNA eukaryotes [3–5,7–9]. In addition, several plant and animal virus, and phage genomes encode topoisomerases [1,2,4,10]. Plant Science 168 (2005)Genomes encounter topological constraints due to the double helical structure of DNA. The two DNA strands in a DNA duplex are topologically linked in prokaryotes due to the circular nature of their chromosomes and plasmids, and in eukaryotes due to DNA binding to nuclear matrix proteins [1–4]. This topological linkage precludes free rotation of the DNA strands around each other in the double helix [1–4]. DNA topoisomerases relieve torsional strain during DNA replication and transcription by opening transient gates in the sugar-phosphate backbone of the DNA molecule and passing another single or double-stranded DNA segment through this gate [2–6]. DNA topoisomerases are ubiquitous occurring in prokaryotes and in nuclei, chloroplasts, and mitochondria of DNA topoisomerases are broadly classified into two families based on the break introduced by the enzyme into a DNA duplex. Type I topoisomerases (Topo I) cleave and reseal only one strand of the DNA duplex to allow passage of another strand. Type II topoisomerases (EC 5.99.1.3) are the only enzymes that generate a staggered double-stranded break (DSB) in DNA, transport a second duplex through the cleavage intermediate, and reseal the DSB in a reaction coupled with ATP hydrolysis [1–4,11]. Topo II functions in multiple processes related to management of genome topology including relaxation of positive DNA supercoils formed during replication and transcription, and untangling daughter DNA molecules during chromosome segregation [3–5]. In eukaryotic cells, Topo II is an abundant chromosomal protein that plays a key role in chromosomal scaffolding, and condensation, suppres