Recently, several studies have found direct interactions between helicases and topoisomerases. However, various differences were found in their mode of function.
Helicase is an unwinding enzyme and it can bind the single strand region of DNA double helix and moves 5′ to 3′ direction. It catalyzes the hydrolysis of ATP and uses this energy to separate the strands during replication. However helicase cannot bind to double helix, so helicase is completely SS DNA binding enzyme.
Helicase is usually hexameric protein having a motor function to cause strand separation.
Each of the DNA strands, in its double helix form, has its own helicase enzyme so that when the helicase carried out unwinding two opposite moving replication forks are generated.
In bacteria, DNA helicase combines with DNA primase to form primosome complex, which is responsible for creating short RNA primer (<15 nucleotides) on single-stranded DNA to elongate the DNA strand.
A DNA topoisomerases have nuclease activity that breaks a phosphodiester bond in DNA strand. This reaction is reversible, hence, the phosphodiester bond reforms when enzyme dissociates from the DNA strand.
Based on their activity topoisomerases have been separated into two main types they are Type-I topoisomerases and Type-II topoisomerases.
It produces transient single-strand break by binding DNA and creates a break on one strand resulting into formation of 5′- phosphotyrosine linkage. Break in phosphodiester backbone allows the two sections of DNA helix on either side of nick to rotate freely related to each other, using the phosphodiester bond in the strand opposite the nick as a swivel point. Based on intermediate formation in their activity type-I topoisomerases further divided into two subtypes. type-IA and type-1B topoisomerases. Type-IA topoisomerases can form a covalent intermediate with the 5′ end of DNA whereas the type-1B topoisomerase can form a covalent intermediate with the 3′ end of DNA. For their activity, Type-I topoisomerases will not use ATP molecule. They can create nicks in DNA and change the linking number by 1 unit.
Different types of reactions catalyzed by Type-I topoisomerases have been noticed. They are given bellow……..
It produces transient double strand in the helix and forms a covalent linkage to both strands of the DNA helix at the same time. This enzyme has ATP hydrolysis activity. Once it binds to the crossing site then it uses ATP as an energy source to fulfill the following reactions.
- Reversibly it breaks first one helix to create a DNA gate
- It breaks the second helix to pass this break
- Finally, it releases the break and dissociates from the DNA
Different types of reactions catalyzed by Type-II topoisomerases have been noticed. They are given bellow……..
The type-II topoisomerase also known as DNA gyrase has described by Martin Gellert from E. coli. This enzyme can introduce the supercoils into DNA. For generating negative supercoil in DNA that uses energy from ATP hydrolysis. It is a tetramer of two different subunits such as GyrA and GyrB subunit.
GyrA has the ability to cut and rejoin the DNA where as GyrB responsible for providing the energy for GyrA reaction by ATP hydrolysis.
The highly potent antibacterial drugs such quinolone antibiotics (nalidixic acid) and fluoroquinolone antibiotics (ciprofloxacin and norfloxacin) can stop the replication by inhibiting DNA gyrase (GyrA subunit) activity, it leads to complete death of bacteria. Whereas aminocoumarin antibiotic (Novobiocin) inhibit the gyrase ATPase activity by binding to GyrB protein and preventing it from binding ATP.
Reaction of topoisomerase
Topoisomerase catalyzes one (or both) strands of the DNA and allowing the free end (or ends) to rotate the helix axis and releasing the break. These enzymes can change the linking number of DNA.
Type IA topoisomerases can change the linking number one and type IB changes the linking number by an integer.
Type IA topoisomerases can change the topology of DNA by changing the linking number by one unit and type IB changes the linking number by an integer.
Type IIA and type IIB topoisomerase can change the topology of DNA by changing the linking number by two units.
Short notes of important features of topoisomerases
Type-I topoisomerases produce transient single strand in the helix, whereas Type-II topoisomerases produce transient double strand.
Type-I topoisomerases enzyme does not require ATP molecule for its function but Type-II topoisomerases require ATP molecule as an energy source to fulfill its function.
The Topoisomerase can change the topology of DNA by changing the linking number.
All type-I topoisomerases cannot carry out the full range of activities. For instant the type-I topoisomerase from E. coli can relax only negatively supercoiled DNA, whereas the same enzyme from calf thymus can relax both negatively and positively supercoiled DNA.
Type-IA topoisomerases create nicks in DNA and change the linking number by 1 unit.
Type-II A and type IIB topoisomerases create breaks in DNA and change the linking number by two units at a time.
Difference between helicase and topoisomerase
1) Topoisomerases can change the linking number and it results in a change in the topological state of the DNA, whereas DNA helicase has no effect on topological parameters.
2) Topoisomerases will not involve in strand separation whereas helicase cause unwinding of the DNA and its leads to strand separation.
3) Topoisomerases can bind to both single strand and double strand DNA molecules, whereas helicase can bind only to single strand regions in double-strand DNA molecule.
4) Topoisomerases may or may not use ATP for their function but helicases have hydrolysis activity, so that they use ATP for their activity.
5) Topoisomerases along with helicases play a major role in replication, generally, topoisomerases act downstream of the DNA helicase so that the positive supercoils generated by helicase activity can be removed.
6) Topoisomerases are swivel proteins whereas helicases are motor proteins and acts on DNA.