ABSTRACT
https://www.niso.org/standards/z39-96/ns/oasis-exchange/table"> DNA replication DNA replication in all organisms proceeds via similar mechanisms. Although the speed of replication can vary, it proceeds by common rules:
Replication is semi-conservative.
All DNA and RNA polymerases synthesize DNA in a 5’ to 3’ direction.
All cellular DNA and RNA polymerases initiate synthesis with an RNA primer.
All DNA and RNA polymerases require magnesium ions to function.
Synthesis of nucleic acids by polymerases All the bacterial nucleic acid polymerases share a common hand-like structure, with the template polynucleotide binding to the palm (the active site) and nucleotides entering between the thumb and forefinger. Bacteria have several DNA polymerases, but only one core RNA polymerase, whereas the eukaryotes have many specialized variants of both. Initiation of DNA replication DNA inside the cell is highly supercoiled, so must be unwound and rewound by topoisomerase I or DNA gyrase as replication proceeds. Bacterial DNA is always replicated from the origin of replication. Two primosomes are formed here and DNA replication occurs bidirectionally. DNA replication fork The DNA replication fork is formed at the origin of replication by the action of DNA helicase and re-annealing of the single strands is prevented by single-stranded binding protein. The opened helix is termed the replication bubble, in which the primosome forms. DNA primase adds a few complementary RNA nucleotides to the template strand, which acts as a primer for the main DNA replication complex, DNA polymerase III. The leading strand is synthesized continuously, but the lagging strand is made in short lengths that are eventually joined together. Primase adds short RNA fragments (Okazaki fragments) to the lagging strand, allowing DNA polymerase III to extend from 5’ to 3’ until it meets the next RNA primer, where extension stops. The short stretches of RNA are then removed by DNA polymerase I and any breaks in the phosphodiester bonds are mended by DNA ligase. Proofreading DNA polymerases I and III both have a separate active site that allows these enzymes to check for perfect complementarity as DNA is synthesized. Termination of synthesis and resolution of replicated circular genomes The movement of the two replisomes is stopped at 180° from ori by the binding of terminator utilization substrate (Tus). This leaves the two complete circular chromosomes intertwined, a situation that is resolved by the action of XerC and XerD at the dif site. Linear genomes The full details of the replication of Bacterial linear genomes have yet to be elucidated but, in Borrelia burgdorferi, a central ori is replicated bidirectionally and terminated by unknown mechanisms. In the bacteriophage cp29 replication is initiated at either end of the chromosome and is terminated in the center by the collision of the two replisomes. Mutation and adaptation Stable inheritance of genetic information is maintained by systems that check and remediate DNA. Microorganisms need these systems to cope with factors such as ultraviolet light and mutagenic chemicals, to prevent induced mutagenesis. Errors in the DNA replication machinery can also cause spontaneous mutagenesis, although in some genomes (at mutational hot spots) this type of mutagenesis seems to be allowed. Any strain derived from this wild type with any change in its genomic make up compared with this wild type is known as a mutant. If the difference in genotype results in an observable change to the properties of the organism, this is a change in phenotype. The mutation of the wild type with a nutritional requirement results in an auxotroph. Related topics (F1) DNA - the primary informational macromolecule (F7) DNA repair(F9) Recombination 117