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Molecule of the Month: DNA topoisomerase	ExPASy Protein Spotlight

DNA Topoisomerase

By Jennifer McDowall

The DNA in the nucleus of a cell contains all the information it requires to carry out life’s processes: growth, development, maintenance, reproduction and protection. With all this information, it is no wonder that the length of a cell’s DNA is far greater than that of the cell compartment that contains it - the DNA in a single human diploid cell contains over 7 billion base pairs divided into 46 chromosomes, which would extend over 2 meters in length if stretched end to end. Yet this massive volume of DNA can be condensed to yield highly compact chromosomes through the tight packing of the DNA: first the DNA is wound around protein nucleosomes like beads on a string, then the beads are coiled into a helical structure, and finally the helical structure is itself supercoiled into a highly-packed coiled-coil structure. This highly compact structure allows the DNA to be safely stored in the nucleus, and to be divided up during cell division without damaging the DNA.

However, such tightly wound DNA does not permit molecules to gain access to individual genes in order to transcribe copies of them, as required for protein synthesis. To overcome this problem, cells use specialised proteins to unwind the DNA in specific regions when it needs access to it, while keeping the rest of the DNA molecule tightly wound and out of harms way. Once the DNA is uncoiled, the DNA double helix itself needs to be unwound to separate it into two individual strands so the information it contains can be accessed. The proteins that carry out this job are collectively known as DNA topoisomerases.

DNA Topoisomerases, Unravelling DNA Strands

DNA topoisomerases are ubiquitous enzymes found in all cell types from viruses to man. These enzymes act to regulate DNA supercoiling by catalysing the winding and unwinding of DNA strands. They do this by making an incision that breaks the DNA backbone, so they can then pass the DNA strands through one another, swivelling and relaxing/coiling the DNA before resealing the breaks. DNA topoisomerases can be divided into two groups based on the number of strands that they break.

Class I DNA Topoisomerases

· Break one strand of a DNA helix.

· Topoisomerases I, III and V.

· ATP independent (except for reverse gyrase).

· Primarily responsible for relaxing positively supercoiled (over-wound) and/or negatively supercoiled (under-wound) DNA, while reverse gyrase can introduce positive supercoils into DNA.

· Mechanism involves rotating the broken strand around the intact strand to relax (unwind) the strain on the DNA helix, followed by resealing the ends of the broken strand.

· Play an important role in DNA replication and transcription (topoisomerase I), and recombination (topoisomerase III).

· Subclasses:

1) Type IA enzymes:

· Bacterial topoisomerase I

· Topoisomerase III

· Reverse gyrase

2) Type IB enzymes:

· Eukaryotic and eukaryal viral topoisomerase I

· Archaeal topoisomerase V

Class II DNA Topoisomerases

· Break two strands of a DNA helix.

· Topoisomerases II (gyrase), IV and VI.

· ATP dependent.

· Responsible for relaxing DNA (topoisomerase IV), as well as introducing either negative (topoisomerase II).

· Mechanism involves passing an intact DNA helix through the gap made by the broken DNA helix, then resealing the strands.

· Play an important role in chromosome condensation (topoisomerase II) and in the segregation of daughter chromosomes during cell division (topoisomerase IV).

· Subclasses:

1) Type IIA enzymes:

· Eukaryotic and eukaryal viral topoisomerase II

· Gyrase (bacterial topoisomerase II)

· Topoisomerase IV

2) Type IIB enzymes:

· Archaeal topoisomerase VI

Next: Functions of DNA Topoisomerases