Editing Plasmid (section)

==Properties and characteristics==
[[File:Plasmid replication (english).svg|400px|thumb|right|There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas [[episomes]], the lower example, can integrate into the host [[chromosome]].]]

In order for plasmids to replicate independently within a cell, they must possess a stretch of DNA that can act as an [[origin of replication]].  The self-replicating unit, in this case, the plasmid, is called a [[Replicon (genetics)|replicon]].  A typical bacterial replicon may consist of a number of elements, such as the gene for plasmid-specific replication initiation protein (Rep), repeating units called [[iteron]]s, [[DnaA]] boxes, and an adjacent AT-rich region.<ref name=Hayes_2003/> Smaller plasmids make use of the host replicative enzymes to make copies of themselves, while larger plasmids may carry genes specific for the replication of those plasmids.  A few types of plasmids can also insert into the host chromosome, and these integrative plasmids are sometimes referred to as [[episome]]s in [[prokaryote]]s.<ref name="brown">{{cite book |chapter-url= https://books.google.com/books?id=yEvt3JdtgTQC&pg=PT26 |title= Gene Cloning and DNA Analysis: An Introduction| vauthors = Brown TA |publisher= Wiley-Blackwell |edition= 6th |year= 2010 |chapter= Chapter 2 – Vectors for Gene Cloning: Plasmids and Bacteriophages |isbn= 978-1405181730}}</ref>

Plasmids almost always carry at least one gene.  Many of the genes carried by a plasmid are beneficial for the host cells, for example: enabling the host cell to survive in an environment that would otherwise be lethal or restrictive for growth.  Some of these genes encode traits for antibiotic resistance or resistance to heavy metal, while others may produce [[virulence factor]]s that enable a bacterium to colonize a host and overcome its defences or have specific metabolic functions that allow the bacterium to utilize a particular nutrient, including the ability to degrade recalcitrant or toxic organic compounds.<ref>{{cite journal | vauthors = Smyth C, Leigh RJ, Delaney S, Murphy RA, Walsh F | title = Shooting hoops: globetrotting plasmids spreading more than just antimicrobial resistance genes across One Health | journal = Microbial Genomics | volume = 8 | issue = 8 | pages = 1–10 | date = August 2022 | pmid = 35960657 | pmc = 9484753 | doi = 10.1099/mgen.0.000858 | doi-access = free }}</ref> Plasmids can also provide bacteria with the ability to [[nitrogen fixation|fix nitrogen]]. Some plasmids, called [[cryptic plasmids]], don't appear to provide any clear advantage to its host, yet still persist in bacterial populations.<ref>{{Cite journal |last1=Fogarty |first1=Emily C. |last2=Schechter |first2=Matthew S. |last3=Lolans |first3=Karen |last4=Sheahan |first4=Madeline L. |last5=Veseli |first5=Iva |last6=Moore |first6=Ryan M. |last7=Kiefl |first7=Evan |last8=Moody |first8=Thomas |last9=Rice |first9=Phoebe A. |last10=Yu |first10=Michael K. |last11=Mimee |first11=Mark |last12=Chang |first12=Eugene B. |last13=Ruscheweyh |first13=Hans-Joachim |last14=Sunagawa |first14=Shinichi |last15=Mclellan |first15=Sandra L. |date=February 2024 |title=A cryptic plasmid is among the most numerous genetic elements in the human gut |journal=Cell |language=en |volume=187 |issue=5 |pages=1206–1222.e16 |doi=10.1016/j.cell.2024.01.039 |pmc=10973873 |pmid=38428395}}</ref> However, recent studies show that they may play a role in antibiotic resistance by contributing to heteroresistance within bacterial populations.<ref>{{cite journal | vauthors = Nicoloff H, Hjort K, Andersson DI, Wang H | title = Three concurrent mechanisms generate gene copy number variation and transient antibiotic heteroresistance | journal = Nature Communications | volume = 15 | issue = 1 | pages = 3981 | date = May 2024 | pmid = 38730266 | pmc = 11087502 | doi = 10.1038/s41467-024-48233-0 | bibcode = 2024NatCo..15.3981N }}</ref>

Naturally occurring plasmids vary greatly in their physical properties.  Their size can range from very small mini-plasmids of less than 1-kilobase pairs (kbp) to very large megaplasmids of several megabase pairs (Mbp).  At the upper end, little differs between a megaplasmid and a [[minichromosome]].  Plasmids are generally circular, but examples of linear plasmids are also known.  These linear plasmids require specialized mechanisms to replicate their ends.<ref name=Hayes_2003>{{cite book | vauthors = Hayes F |chapter= Chapter 1 – The Function and Organization of Plasmids |chapter-url= https://books.google.com/books?id=r6QC0hTwsrwC&pg=PA2 | veditors = Casali N, Presto A |title= E. Coli Plasmid Vectors: Methods and Applications  |series= Methods in Molecular Biology |volume=235|publisher= Humana Press |year= 2003  |pages= 1–5 |isbn= 978-1-58829-151-6}}</ref>

Plasmids may be present in an individual cell in varying number, ranging from one to several hundreds. The normal number of copies of plasmid that may be found in a single cell is called the [[plasmid copy number]], and is determined by how the replication initiation is regulated and the size of the molecule. Larger plasmids tend to have lower copy numbers.<ref name="brown"/> Low-copy-number plasmids that exist only as one or a few copies in each bacterium are, upon [[cell division]], in danger of being lost in one of the segregating bacteria. Such single-copy plasmids have systems that attempt to actively distribute a copy to both daughter cells. These systems, which include the [[parABS system]] and [[parMRC system]], are often referred to as the [[Plasmid partition system|partition system]] or partition function of a plasmid.<ref>{{cite journal | vauthors = Dmowski M, Jagura-Burdzy G | title = Active stable maintenance functions in low copy-number plasmids of Gram-positive bacteria I. Partition systems | journal = Polish Journal of Microbiology | volume = 62 | issue = 1 | pages = 3–16 | date = 2013 | pmid = 23829072 | doi = 10.33073/pjm-2013-001 | doi-access = free }}</ref>
{{Further|Regulatory region of repBA gene}}

Plasmids of ''linear'' form are unknown among [[phytopathogen]]s with one exception, ''[[Rhodococcus fascians]]''.<ref name = "Coup-d-Etat" >{{cite journal | vauthors = Stes E, Vandeputte OM, El Jaziri M, Holsters M, Vereecke D | title = A successful bacterial coup d'état: how Rhodococcus fascians redirects plant development | journal = Annual Review of Phytopathology | volume = 49 | issue = 1 | pages = 69–86 | date = 2011 | pmid = 21495844 | doi = 10.1146/annurev-phyto-072910-095217 | publisher = [[Annual Reviews (publisher)|Annual Reviews]] | bibcode = 2011AnRvP..49...69S }}</ref>