Origin of replication

The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated.^[1] 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.^{[citation needed]}

DNA replication may proceed from this point bidirectionally or unidirectionally.^{[citation needed]}

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^[2]). The origin of replication binds the pre-replication complex, a protein complex that recognizes, unwinds, and begins to copy DNA.^{[citation needed]}

Types

The origin of replication are classified in two ways:

Narrow or broad host range
High- or low-copy number.

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.^[3]
Most archaea have a single circular molecule of DNA, and several origins of replication along this circular chromosome.^[4]
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.^[5] 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.

Origins of replication are typically assigned names containing "ori".

Prokaryotic

Bacterial Genome Origins

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 .^[6]

Bacterial Plasmid Origins

Many bacteria, including E. coli, contain plasmids that each contain an origin of replication. These are separate from the origins of replication that are used by the bacteria to copy their genome and often function very differently. For example, the E. coli plasmid pBR322 uses a protein called Rop/Rom to regulate the number of plasmids that are within each bacterial cell ^{[citation needed]}. The most common origin of replication that is used in plasmids for genetic engineering is called pUC. This origin is derived from pBR322 but it contains two mutations. One single point mutation in the origin itself and another that deletes the Rop/Rom gene. This removes all the regulatory constraints on the plasmids replication and the bacteria then go from producing 30-40 plasmids per cell with pBR322 up to producing over 500 with pUC. This allows genetic engineers to produce large quantities of DNA for research purposes. Other origins of 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).^[7]

Eukaryotic

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.^{[citation needed]}

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):^{[citation needed]}

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.^{[citation needed]}

In humans an origin of replication has been originally identified near the Lamin B2 gene on chromosome 19 and the ORC binding to it has extensively been studied.^[8]

Viral

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.

References

^ Technical Glossary Edward K. Wagner, Martinez Hewlett, David Bloom and David Camerini Basic Virology Third Edition, Blackwell publishing, 2007 ISBN 1-4051-4715-6
^ http://nar.oxfordjournals.org/content/34/2/564.full
^ Mott ML, Berger JM (2007). "DNA replication initiation: mechanisms and regulation in bacteria". Nat. Rev. Microbiol. 5 (5): 343–54. doi:10.1038/nrmicro1640. PMID 17435790.
^ Kelman LM, Kelman Z (2004). "Multiple origins of replication in archaea". Trends Microbiol. 12 (9): 399–401. doi:10.1016/j.tim.2004.07.001. PMID 15337158.
^ Nasheuer HP, Smith R, Bauerschmidt C, Grosse F, Weisshart K (2002). "Initiation of eukaryotic DNA replication: regulation and mechanisms". Prog. Nucleic Acid Res. Mol. Biol. 72: 41–94. doi:10.1016/S0079-6603(02)72067-9. PMID 12206458.
^ Baker TA, Wickner SH (1992). "Genetics and enzymology of DNA replication in Escherichia coli". Annual Review of Genetics. 26: 447–77. doi:10.1146/annurev.ge.26.120192.002311. PMID 1482121.
^ oxfordgenetics.com/origins,.
^ Falaschi A, Giacca M. The quest for a human ori, 'Genetica',1994;94(2-3):255-66

External links

Ori-Finder, an online software for prediction of bacterial and archaeal oriCs
Replication+Origin at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

[1] Technical Glossary Edward K. Wagner, Martinez Hewlett, David Bloom and David Camerini Basic Virology Third Edition, Blackwell publishing, 2007 ISBN 1-4051-4715-6

[2] ttp://nar.oxfordjournals.org/content/34/2/564.full

[3] Mott ML, Berger JM (2007). "DNA replication initiation: mechanisms and regulation in bacteria". Nat. Rev. Microbiol. 5 (5): 343–54. doi:10.1038/nrmicro1640. PMID 17435790.

[4] Kelman LM, Kelman Z (2004). "Multiple origins of replication in archaea". Trends Microbiol. 12 (9): 399–401. doi:10.1016/j.tim.2004.07.001. PMID 15337158.

[5] Nasheuer HP, Smith R, Bauerschmidt C, Grosse F, Weisshart K (2002). "Initiation of eukaryotic DNA replication: regulation and mechanisms". Prog. Nucleic Acid Res. Mol. Biol. 72: 41–94. doi:10.1016/S0079-6603(02)72067-9. PMID 12206458.

[pmid1482121-6] Baker TA, Wickner SH (1992). "Genetics and enzymology of DNA replication in Escherichia coli". Annual Review of Genetics. 26: 447–77. doi:10.1146/annurev.ge.26.120192.002311. PMID 1482121.

[Origin_Copy_Number-7] xfordgenetics.com/origins,.

[human_ori-8] Falaschi A, Giacca M. The quest for a human ori, 'Genetica',1994;94(2-3):255-66

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