Editing Plasmid (section)

== Plasmids in nature ==

=== Yeast plasmids ===
[[Yeast]]s naturally harbour various plasmids. Notable among them are 2&nbsp;μm plasmids—small circular plasmids often used for [[genetic engineering]] of yeast—and linear pGKL plasmids from ''[[Kluyveromyces lactis]]'', that are responsible for [[killer phenotypes]].<ref>{{cite journal | vauthors = Gunge N, Murata K, Sakaguchi K | title = Transformation of Saccharomyces cerevisiae with linear DNA killer plasmids from Kluyveromyces lactis | journal = Journal of Bacteriology | volume = 151 | issue = 1 | pages = 462–464 | date = July 1982 | pmid = 7045080 | pmc = 220260 | doi = 10.1128/JB.151.1.462-464.1982 }}</ref>

Other types of plasmids are often related to yeast cloning vectors that include:
* ''Yeast integrative plasmid (YIp)'', yeast vectors that rely on integration into the host chromosome for survival and replication, and are usually used when studying the functionality of a solo gene or when the gene is toxic. Also connected with the gene URA3, that codes an enzyme related to the biosynthesis of pyrimidine nucleotides (T, C);
* ''Yeast Replicative Plasmid (YRp)'', which transport a sequence of chromosomal DNA that includes an origin of replication. These plasmids are less stable, as they can be lost during budding.

=== Plant mitochondrial plasmids ===
The mitochondria of many higher plants contain [[Replicon (genetics)|self-replicating]], extra-chromosomal linear or circular DNA molecules which have been considered to be plasmids. These can range from 0.7 kb to 20 kb in size. The plasmids have been generally classified into two categories- circular and linear.<ref name="Gualberto-2014">{{cite journal | vauthors = Gualberto JM, Mileshina D, Wallet C, Niazi AK, Weber-Lotfi F, Dietrich A | title = The plant mitochondrial genome: dynamics and maintenance | journal = Biochimie | volume = 100 | pages = 107–120 | date = May 2014 | pmid = 24075874 | doi = 10.1016/j.biochi.2013.09.016 }}</ref> Circular plasmids have been isolated and found in many different plants, with those in ''[[Vicia faba]] and [[Chenopodium album]]'' being the most studied and whose mechanism of replication is known. The circular plasmids can replicate using the θ model of replication (as in ''Vicia faba'') and through [[rolling circle replication]] (as in ''C.album'').<ref>{{cite journal | vauthors = Backert S, Meissner K, Börner T | title = Unique features of the mitochondrial rolling circle-plasmid mp1 from the higher plant Chenopodium album (L.) | journal = Nucleic Acids Research | volume = 25 | issue = 3 | pages = 582–589 | date = February 1997 | pmid = 9016599 | pmc = 146482 | doi = 10.1093/nar/25.3.582 }}</ref> Linear plasmids have been identified in some plant species such as ''[[Beta vulgaris]]'', ''[[Brassica napus]], [[Maize|Zea mays]]'', etc. but are rarer than their circular counterparts.

The function and origin of these plasmids remains largely unknown. It has been suggested that the circular plasmids share a common ancestor, some genes in the mitochondrial plasmid have counterparts in the nuclear DNA suggesting inter-compartment exchange. Meanwhile, the linear plasmids share structural similarities such as invertrons with viral DNA and fungal plasmids, like fungal plasmids they also have low GC content, these observations have led to some hypothesizing that these linear plasmids have viral origins, or have ended up in plant mitochondria through [[horizontal gene transfer]] from pathogenic fungi.<ref name="Gualberto-2014" /><ref>{{cite journal | vauthors = Handa H | title = Linear plasmids in plant mitochondria: peaceful coexistences or malicious invasions? | journal = Mitochondrion | volume = 8 | issue = 1 | pages = 15–25 | date = January 2008 | pmid = 18326073 | doi = 10.1016/j.mito.2007.10.002 }}</ref>