Editing Plasmid (section)

==Classifications and types==
[[File:Conjugation.svg|right|250px|thumb|Overview of bacterial conjugation]]
[[File:DNA Under electron microscope Image 3576B-PH.jpg|thumb|[[Electron micrograph]] of a DNA fiber bundle, presumably of a single bacterial chromosome loop]]
[[File:Plasmid em-en.jpg|thumb|Electron micrograph of a bacterial DNA plasmid (chromosome fragment)]]
Plasmids may be classified in a number of ways.  Plasmids can be broadly classified into conjugative plasmids and non-conjugative plasmids.  Conjugative plasmids contain a set of [[transfer gene]]s which promote sexual conjugation between different cells.<ref name="brown"/> In the complex process of [[Bacterial conjugation|conjugation]], plasmids may be transferred from one bacterium to another via [[Pilus#Conjugative pili|sex pili]] encoded by some of the transfer genes (see figure).<ref>{{cite book |url=https://books.google.com/books?id=Mhs-P94d1R8C&pg=PA795 |title=Molecular Biology | vauthors = Clark DP, Pazdernik NJ |page=795 |edition=2nd |publisher=Academic Cell |year= 2012 |isbn=978-0123785947 }}</ref> Non-conjugative plasmids are incapable of initiating conjugation, hence they can be transferred only with the assistance of conjugative plasmids.  An intermediate class of plasmids are mobilizable, and carry only a subset of the genes required for transfer. They can parasitize a conjugative plasmid, transferring at high frequency only in its presence.<ref>{{cite journal |last1=Udo |first1=E.E. |last2=Jacob |first2=L.E. |title=Conjugative Transfer of High-Level Mupirocin Resistance and the Mobilization of Non-Conjugative Plasmids in Staphylococcus aureus |journal=Microbial Drug Resistance |date=January 1998 |volume=4 |issue=3 |pages=185–193 |doi=10.1089/mdr.1998.4.185 |pmid=9818970 }}</ref>

Plasmids can also be classified into incompatibility groups.  A microbe can harbour different types of plasmids, but different plasmids can only exist in a single bacterial cell if they are compatible.  If two plasmids are not compatible, one or the other will be rapidly lost from the cell. Different plasmids may therefore be assigned to different incompatibility groups depending on whether they can coexist together.  Incompatible plasmids (belonging to the same incompatibility group) normally share the same replication or partition mechanisms and can thus not be kept together in a single cell.<ref>{{cite book | vauthors = Radnedge L, Richards H | chapter = Chapter 2: The Development of Plasmid Vectors. | chapter-url=https://books.google.com/books?id=w0jvDl0zJPIC&pg=PA76 | date = January 1999 | volume = 29 | pages = 51–96 (75–77) | veditors = Smith MC, Sockett RE |title=Genetic Methods for Diverse Prokaryotes |series=Methods in Microbiology |publisher= Academic Press |isbn= 978-0-12-652340-9 }}</ref><ref>{{cite web|url=http://blog.addgene.org/plasmid-101-origin-of-replication|title=Plasmids 101: Origin of Replication |website=addgene.org}}</ref> Incompatibility typing (or Inc typing) was traditionally achieved by genetic phenotyping methods, testing whether cells stably transmit plasmid pairs to their progeny.<ref name="Johnson_2009">{{cite book | vauthors = Johnson TJ, Nolan LK | title = Plasmid replicon typing | series = Methods in Molecular Biology (Clifton, N.J.) | volume = 551 | pages = 27–35 | date = 2009 }}</ref> This has largely been superseded by genetic methods such as PCR, and more recently by whole-genome sequencing methods with bioinformatic tools such as PlasmidFinder.<ref name="Carattoli_2014">{{cite journal | vauthors = Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H | title = In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing | journal = Antimicrobial Agents and Chemotherapy | volume = 58 | issue = 7 | pages = 3895–3903 | date = 2014 | doi = 10.1128/AAC.02412-14 | pmid = 24777092 | pmc = 4068535 }}</ref>

Another way to classify plasmids is by function. There are five main classes:
* Fertility [[F-plasmid]]s, which contain ''tra'' genes. They are capable of [[bacterial conjugation|conjugation]] and result in the expression of [[Pilus#Conjugative pili|sex pili]].<ref name="Helinski_2022" /><ref name=":0">{{cite journal | vauthors = Watanabe T, Nishida H, Ogata C, Arai T, Sato S | title = EPISOME-MEDIATED TRANSFER OF DRUG RESISTANCE IN ENTEROBACTERIACEAE. VII. TWO TYPES OF NATURALLY OCCURRING R FACTORS | journal = Journal of Bacteriology | volume = 88 | issue = 3 | pages = 716–726 | date = September 1964 | pmid = 14208512 | pmc = 277371 | doi = 10.1128/jb.88.3.716-726.1964 }}</ref> F-plasmids are categorized as either (+) or (-) and contribute to the difference of being a donor or recipient during conjugation.<ref name="Helinski_2022" /><ref name=":0" /><ref>{{Cite journal |last1=Meynell |first1=Elinor |last2=Datta |first2=Naomi |date=February 1966 |title=The relation of resistance transfer factors to the F-factor (sex-factor) of Escherichia coli K12 |journal=Genetics Research |language=en |volume=7 |issue=1 |pages=134–140 |doi=10.1017/S0016672300009538 |pmid=5324663 |doi-access=free }}</ref>
* Resistance (R) plasmids, which contain genes that provide resistance against [[antibiotic]]s or antibacterial agents was first discovered in 1959.<ref>{{cite journal |last1=Datta |first1=N. |title=Classification of plasmids as an aid to understanding their epidemiology and evolution |journal=Journal of Antimicrobial Chemotherapy |date=1977 |volume=3 |issue=suppl C |pages=19–23 |doi=10.1093/jac/3.suppl_c.19 |pmid=599130 }}</ref> R-factors where seen as the contributing factor for the spread of [[Multiple drug resistance|multidrug resistance]] in bacteria, some R-plasmids assist in transmissibility of other specifically non- self transmissible R-factors.<ref>{{cite journal |last1=Watanabe |first1=Tsutomu |title=Infective Heredity of Multiple Drug Resistance in Bacteria |journal=Bacteriological Reviews |date=1963 |volume=27 |issue=1 |pages=87–115 |doi=10.1128/mmbr.27.1.87-115.1963 |pmid=13999115 |pmc=441171 }}</ref><ref>{{cite journal |last1=Anderson |first1=E. S. |last2=Lewis |first2=M. J. |title=Characterization of a Transfer Factor Associated with Drug Resistance in Salmonella typhimurium |journal=Nature |date=November 1965 |volume=208 |issue=5013 |pages=843–849 |doi=10.1038/208843a0 |pmid=5331112 |bibcode=1965Natur.208..843A }}</ref> Historically known as R-factors, before the nature of plasmids was understood. 
* Col plasmids, which contain genes that code for [[bacteriocin]]s, [[protein]]s that can kill other bacteria.
* Degradative plasmids, which enable the digestion of unusual substances, e.g. [[toluene]] and [[salicylic acid]].
* Virulence plasmids, which turn the bacterium into a [[pathogen]]. e.g. [[Ti plasmid]] in ''[[Agrobacterium tumefaciens]].'' Bacteria under selective pressure will keep plasmids containing virulence factors as it is a cost - benefit for survival, removal of the selective pressure can lead to the loss of a plasmid due to the expenditure of energy needed to keep it is no longer justified.<ref name=":1" /><ref>{{cite book |doi=10.1016/b978-0-12-813288-3.00035-5 |chapter=Preface to Third Edition |title=Molecular Biology |date=2019 |last1=Clark |first1=David P. |last2=Pazdernik |first2=Nanette J. |last3=McGehee |first3=Michelle R. |pages=xiii-xiv |isbn=978-0-12-813288-3 }}</ref>

Plasmids can belong to more than one of these functional groups.

===Sequence-based plasmid typing===
With the wider availability of whole genome sequencing which is able to capture the genetic sequence of plasmids, methods have been developed to cluster or type plasmids based on their sequence content. Plasmid multi-locus sequence typing (pMLST) is based on chromosomal [[Multilocus sequence typing]] by matching the sequence of replication machinery genes to databases of previously classified sequences. If the sequence [[allele]] matches the database, this is used as the plasmid classification, and therefore has higher sensitivity than a simple presence or absence test of these genes.<ref name="Carattoli_2014" />

A related method is to use [[average nucleotide identity]] between plasmids to find close genetic neighbours. Tools which use this approach include COPLA<ref name="RedondoSalvo_2021">{{cite journal | vauthors = Redondo-Salvo S, Bartomeus-Peñalver R, Vielva L, Tagg KA, Webb HE, Fernández-López R, de la Cruz F | title = COPLA, a taxonomic classifier of plasmids | journal = BMC Bioinformatics | volume = 22 | issue = 1 | pages = 390 | date = 2021 | doi = 10.1186/s12859-021-04299-x | doi-access = free | pmid = 34332528 | pmc = 8325299 }}</ref> and MOB-cluster.<ref name="Robertson_2018">{{cite journal | vauthors = Robertson J, Nash J | title = MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies | journal = Microbial Genomics | volume = 4 | issue = 8 | date = 2018 | doi = 10.1099/mgen.0.000206 | doi-access = free | pmid = 30052170 | pmc = 6159552 }}</ref>

Creating typing classifications using [[unsupervised learning]], that is without a pre-existing database or 'reference-free', has been shown to be useful in grouping plasmids in new datasets without biasing or being limited to representations in a pre-built database—tools to do this include mge-cluster.<ref name="ArredondoAlonso_2023">{{cite journal | vauthors = Arredondo-Alonso S, Gladstone RA, Pöntinen AK, Gama JA, Schürch AC, Lanza VF, Johnsen PJ, Samuelsen Ø, Tonkin-Hill G, Corander J | title = Mge-cluster: a reference-free approach for typing bacterial plasmids | journal = NAR Genomics and Bioinformatics | volume = 5 | issue = 3 | pages = lqad066 | date = 2023 | doi = 10.1093/nargab/lqad066 | pmid = 37435357 | pmc = 10331934 }}</ref> As plasmid frequently change their gene content and order, modelling genetic distances between them using methods designed for point mutations can lead to poor estimates of the true evolutionary distance between plasmids. Tools such as pling find homologous sequence regions between plasmids, and more accurately reconstruct the number of evolutionary events ([[structural variants]]) between each pair, then use unsupervised clustering apporaches to group plasmids.<ref name="Frolova_2024">{{cite journal | vauthors = Frolova D, Lima L, Roberts LW, Bohnenkämper L, Wittler R, Stoye J, Iqbal Z | title = Applying rearrangement distances to enable plasmid epidemiology with pling | journal = Microbial Genomics | volume = 10 | issue = 10 | pages = 001300 | date = 2024 | doi = 10.1099/mgen.0.001300 | doi-access = free | pmid = 39401066 | pmc = 11472880 }}</ref>

===RNA plasmids===
Although most plasmids are double-stranded DNA molecules, some consist of [[single-stranded DNA]], or predominantly [[double-stranded RNA]]. RNA plasmids are non-infectious extrachromosomal linear RNA replicons, both [[Virus-like particle|encapsidated]] and unencapsidated, which have been found in fungi and various plants, from algae to land plants. In many cases, however, it may be difficult or impossible to clearly distinguish RNA plasmids from RNA viruses and other infectious RNAs.<ref name = "Brown_1989">{{cite book | vauthors = Brown GG, Finnegan PM | title = RNA Plasmids | series = [[International Review of Cytology]] | volume = 117 | pages = 1–56 | date = January 1989 | pmid = 2684889 | doi = 10.1016/s0074-7696(08)61333-9 | isbn = 978-0-12-364517-3 }}</ref>

===Chromids===
{{main|Chromid}}
Chromids are elements that exist at the boundary between a [[chromosome]] and a plasmid, found in about 10% of bacterial species sequenced by 2009. These elements carry core genes and have [[codon usage]] similar to the chromosome, yet use a plasmid-type replication mechanism such as the low copy number RepABC. As a result, they have been variously classified as minichromosomes or megaplasmids in the past.<ref>{{cite journal | vauthors = Harrison PW, Lower RP, Kim NK, Young JP | title = Introducing the bacterial 'chromid': not a chromosome, not a plasmid | journal = Trends in Microbiology | volume = 18 | issue = 4 | pages = 141–148 | date = April 2010 | pmid = 20080407 | doi = 10.1016/j.tim.2009.12.010 }}</ref> In ''[[Vibrio]]'', the bacterium synchronizes the replication of the chromosome and chromid by a conserved genome size ratio.<ref name=Bruhn>{{cite journal | vauthors = Bruhn M, Schindler D, Kemter FS, Wiley MR, Chase K, Koroleva GI, Palacios G, Sozhamannan S, Waldminghaus T | title = Functionality of Two Origins of Replication in ''Vibrio cholerae'' Strains With a Single Chromosome | journal = Frontiers in Microbiology | volume = 9 | pages = 2932 | date = 30 November 2018 | pmid = 30559732 | pmc = 6284228 | doi = 10.3389/fmicb.2018.02932 | doi-access = free }}</ref>