Origin of replication
The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated. This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.
DNA replication may proceed from this point bidirectionally or unidirectionally.
The specific structure of the origin of replication varies somewhat from species to species, but all share some common characteristics such as high AT content (repeats of adenine and thymine are easier to separate because their base stacking interactions are not as strong as those of guanine and cytosine). The origin of replication binds the pre-replication complex, a protein complex that recognizes, unwinds, and begins to copy DNA.
There are also significant differences between prokaryotic and eukaryotic origins of replication:
- Most bacteria have a single circular molecule of DNA, and typically only a single origin of replication per circular chromosome.
- Most archaea have a single circular molecule of DNA, and several origins of replication along this circular chromosome.
- Eukaryotes often have multiple origins of replication on each linear chromosome that initiate at different times (replication timing), with up to 100,000 present in a single human cell. Having many origins of replication helps to speed the duplication of their (usually) much larger store of genetic material. The segment of DNA that is copied starting from each unique replication origin is called a replicon. The replicons range from 40 kb length, in yeast and Drosophila, to 300 kb in plants.
- Mitochondrial DNA in many organisms has two ori sequences. In humans, they are called oriH and oriL for the heavy and light strand of the DNA, each being the origin of replication for single-stranded replication. The two Chloroplast DNA ori sequences in Nicotiana tabacum, the tobacco plant, has been characterized as oriA and oriB.
Origins of replication are typically assigned names containing "ori". When it comes to plasmids, origins of replication are classified in two ways:
- Narrow or broad host range
- High- or low-copy number.
The genome of E. coli consists of a single circular DNA molecule of approximately 4.6 x 106 nucleotide pairs. DNA replication typically begins at a single origin of replication. In E. coli, the origin of replication—oriC—consists of three A–T rich 13-mer repeats and four 9-mer repeats. Ten to 20 monomers of the replication initiator protein DnaA bind to the 9-mer repeats, and the DNA coils around this protein complex forming a protein core. This coiling stimulates the AT rich region in the 13-mer sequence to unwind, allowing the helicase loader DnaC to load the replicative helicase DnaB to each of the two unwound DNA strands. The helicase DnaB forms the basis of the primosome, a complex of enzymes to which DNA polymerase III is recruited before replication can occur.
Many bacteria, including E. coli, contain plasmids that each contain an origin of replication, usually named oriV for vegetative replication. They in general still work by binding DnaA. These are separate from the origins of replication that are used by the bacteria to copy their genome and are regulated differently. For example, the E. coli plasmid pBR322 uses a protein called Rop/Rom (derived from pMB1, a relative of ColE1) to regulate the number of plasmids that are within each bacterial cell. This limits the number of plasmids per cell – the copy number – to 30–40. The pUC series of plasmids, including pUC19, is more commonly used. Compared to pBR322, it uses ori with a single point mutation and has the regulatory Rop/Rom gene removed. With those changes, the bacteria can produce up to 500 copies pUC19 per cell. This allows genetic engineers to produce large quantities of DNA for research purposes. Other origins of plasmid replication include pSC101 (derived from Salmonella, around 5 copies per cell), 15A origin (derived from p15A, 10–20 copies per cell) and Bacterial artificial chromosomes (1 copy per cell).
In eukaryotes, the budding yeast Saccharomyces cerevisiae were first identified by their ability to support the replication of mini-chromosomes or plasmids, giving rise to the name Autonomously replicating sequences or ARS elements. Each budding yeast origin consists of a short (~11 bp) essential DNA sequence (called the ARS consensus sequence or ACS) that recruits replication proteins.
In other eukaryotes, including humans, the base pair sequences at the replication origins vary. Despite this sequence variation, all the origins form a base for assembly of a group of proteins known collectively as the pre-replication complex (pre-RC):
- First, the origin DNA is bound by the origin recognition complex (ORC) which, with help from two further protein factors (Cdc6 and Cdt1), load the mini chromosome maintenance (or MCM) protein complex.
- Once assembled, this complex of proteins indicates that the replication origin is ready for activation. Once the replication origin is activated, the cell's DNA will be replicated.
In metazoans, pre-RC formation is inhibited by the protein geminin, which binds to and inactivates Cdt1. Regulation of replication prevents the DNA from being replicated more than once each cell cycle.
Viruses often possess a single origin of replication.
A variety of proteins have been described as being involved in viral replication. For instance, Polyoma viruses utilize host cell DNA polymerases, which attach to a viral origin of replication if the T antigen is present.
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