DNA replication in E. coli
DNA replication in E. coli: Pre-primosome by Allen Gathman, on Flickr
E. coli DNA is a single, circular, double stranded DNA molecule.
C" is a sequence in the DNA where replication begins. "oriC" is not a gene just a place where a protein binds to the DNA. The protein dnaA binds to the ori
C, and other proteins, such as dnaB (helicase) and dnaC, bind to the dnaA. dnaC leaves dnaA forming the pre-primosome. dnaA is unable to synthesize without a primer on it.
dnaA originally starts separating the strands at oriC
but once dnaB arrives, dnaA is no longer needed and dnaA leaves leaving dnaB responsible for the remainder of denaturation during replication. dnaC is needed because it brings dnaB to dnaA,dnaC is also necessary for dnaB's bindingto "oriC", and dnaB cannot function until dnaC leaves.
Because not only dnaC and dnaB bind to dnaA, dnaA is said to function similarly as a nucleus because others bind to it. This function creates the preprimosome.
Local Denaturation of DNA
DNA replication in E. coli: Pre-primosomes by Allen Gathman, on Flickr
is a gene that codes for the protein dnaA which binds to the oriC
. This binding promotes denaturation of the strands, and so dnaB and dnaC binds to the single-strand formed. The dnaC then detaches and dnaB (it's a helicase) unwinds the strands of the denatured region, opening the replication fork. Two dnaB bind at oriC
at each strand forming the basis of replisomes.
DNA replication in E. coli: The primosome by Allen Gathman, on Flickr
After a replication fork has been formed, dnaA is removed. A protein called dnaG now binds, creating a primosome (dnaB, dnaG, and more proteins). dnaG is also known as primase, which is an RNA polymerase. So, the primase synthesizes a short piece of RNA; RNA then acts as a primer for DNA synthesis. Also the DNA polymerase require primers with 3' ends on them or the process cannot begin.
DNA replication in E. coli: Replication fork by Allen Gathman, on Flickr
A replisome is when two Pol III (DNA polymerase III) joins a primosome, and it is what actually does DNA synthesis. It adds dNTPs to the RNA primer, which synthesizes new DNA in the 5'-3' direction, complementary to the template strand. Another primer was made on oriC
which is problematic since strands in DNA are anti-parallel, causing the primer to point in a 3'-5' direction: DNA can not be synthesized in this direction because polymerase can only add new nucleotides to an existing strand of DNA primer on the 3' end.
DNA replication in E. coli: Fork movement by Allen Gathman, on Flickr
Replisome also includes dnaB and dnaC which constitutes helicase. It separates the strands further, moving the fork to the right.
A new primer is formed for the bottom "lagging" strand in the replication fork. After about 1000 nucleotides, another RNA primer will be formed. The bottom strand is made in pieces referred to as "Okazaki fragments". The top "leading" strand is made continuously.
DNA replication in E. coli: Bidirectional replication by Allen Gathman, on Flickr
This picture shows a DNA molecule that is half replicated. The strand that is synthesized in the same direction as the fork is called the leading strand. The lagging strand, however, does not move in the direction in which the fork moves. The two forks move in opposite directions meaning that the leading and lagging strands are also moving in the opposite direction.
DNA Gyrase is a Type II topoisomerase that catalyzes the introduction of negative supercoiling in DNA, in other words it removes supercoils. Here's a video
explaining its action.
DNA gyrase introduces negative supercoils into DNA by looping the template so as to form a crossing, then cutting one of the double helices and passing the other through it before releasing the break. Each time DNA gyrase performs this action, there is a net change of -1 turn in DNA supercoiling.