Coordinated regulation of gene expression by E ... - Jacobs University

INTRODUCTION
have more base-pairs than there would be in a relaxed molecule of DNA (10.4 bp/turn).
The superhelical tension can be relieved by nicking one of the strands of DNA, rotating
and re-ligating the strands. The other option would be to convert the helical tension of
the twist into writhe, by which the DNA attains the supercoiled form. The writhe in the
case of negative supercoiling will be right-handed. The DNA is said to be positively
supercoiled when there are fewer base-pairs per helical turn compared to a relaxed
molecule. The superhelical tension of twist in this case can be relieved by introducing
left-handed writhe.
The supercoiling of the DNA can be described using three parameters: [1]
Linking number (Lk) – an integer value which refers to the number of times the two
strands make a 360 o turn [2] Twist (Tw) – a real number denoting the winding of
strands around the helical axis [3] Writhe (Wr) – a real number which denotes the
supercoils in the DNA. The three parameters are related as follows: Linking number =
Twist + Writhe (Lk = Tw + Wr). As said before, most DNA in vivo is negatively
supercoiled. The relative degree to which a molecule is supercoiled can be expressed as
the specific linking difference or superhelical density (σ). This quantity gives a lengthindependent
measure of the level of supercoiling, σ = (Lk - Lk o )/Lk o .
According to ‘twin supercoiled domain’ model, transcription generates positive
supercoils in front of the transcribing RNAP complex and negative supercoiling behind
it [Liu and Wang, 1987; Wu et al., 1988]. Topoisomerases are the enzymes which take
care of these two domains of superhelical tension. There are four topoisomerases in
E.coli. Topoisomerase II (gyrase, product of gyrA and gyrB genes) introduces negative
supercoils while the other three topoisomerases, topoisomerase I (topA gene product),
III (topB gene product) and IV (parC and parE gene product) relax negative supercoils.
Gyrase, topoisomerase I & IV are held responsible for maintaining the supercoiled state
of the DNA while topoisomerases III mainly manages decatenation reactions [Hiasa and
Marians, 1994].
The negatively supercoiled DNA inside the cell is maintained at a steady state
level by the actions of gyrase, topoisomerases I and topoisomerase IV [ Menzel et al.,
1983; Zechiedrich et al., 2000] within + 15% range of normal mean value [Drlica et al.,
1992]. The feedback mechanisms involved in the expression of gyrA, gyrB (active at
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