Other plasmids found were IncB/O/K/Z, IncR, IncN and P0111 as well as some plasmids containing mainly phage like genes (phage/phage plasmid) (8 out of 42 plasmids). Palmer K. L., Kos V. N., Gilmore M. S. (2010). Similarly, the Rep proteins of Inc4, Inc9, Inc10, and Inc14 plasmids have 311314 amino acid sequences and share a high degree of identity (>75%) with each other. Plasmids are transmissible by conjugation (Frost et al., 2005; Sota and Top, 2008; Frost and Koraimann, 2010 ). Molecular characterization of three plasmids from. IncP-1epsilon plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes, Horizontal gene transfer between bacteria, Plasmids foster diversification and adaptation of bacterial populations in soil. [45] For this reason, organelle DNA, including mtDNA, is inherited from the mother. A short single-stranded DNA sequence used as an initiation point for PCR amplification or sequencing. In the GenBank database, 166 plasmids were found in Lactobacillus, and notably, multiple (five to ten) plasmids were found in individual strains, such as Lactobacillus fermentum MTCC 8711 (Jayashree et al., 2013), Lactobacillus plantarum 16 (Crowley et al., 2013), and Lactobacillus reuteri I5007 (Hou et al., 2014). Biologydictionary.net, November 16, 2016. https://biologydictionary.net/plasmid/. 2.4C: Plasmids and Transposons - Biology LibreTexts Not all are R plasmids. Burmolle M., Norman A., Sorensen S. J., Hansen L. H. (2012). The classification based on the replicon typing is also useful for grouping the plasmids in unidentified Inc groups. [27][28][29] A recent theory that questions the current standard model of ring shaped chloroplast DNA (cpDNA), suggests that cpDNA may more commonly take a linear shape. B. burgdorferi type strain B31, the causative agent of Lyme disease, possesses twelve linear plasmids and nine circular plasmids (Fraser et al., 1997; Casjens et al., 2000). Similar plasmids are also found in Bacillus (Guglielmetti et al., 2007) and several genera in Actinobacteria (Ventura et al., 2007). A transposon contains a number of genes, coding for antibiotic resistance or other traits, flanked at both ends by insertion sequences coding for an enzyme called transpoase. Some resistance plasmids can transfer themselves through conjugation. Rolling circle-replicating plasmids from gram-positive and gram-negative bacteria: a wall falls. There were large differences in the average sizes and GC contents between the two phyla. Shintani M., Ohtsubo Y., Fukuda K., Hosoyama A., Ohji S., Yamazoe A., et al.. (2014b). Thus, the resolution of a gel decreases with increased voltage. A pRN-type plasmid, pSSVx, is known to be a virus-plasmid hybrid that coexists intracellularly with the fusellovirus SSV1 and can be packaged into viral particles (Arnold et al., 1999). Most chloroplasts house all of their genetic material in a single ringed chromosome, however in some species there is evidence of multiple smaller ringed plasmids. As described above, classification of plasmids based on their MOB types and MPF classes has previously been reported (Garcilln-Barcia et al., 2009, 2011; Smillie et al., 2010). Community-wide plasmid gene mobilization and selection. Before A. Within this phylum, 1077 plasmids were classified using previously known Rep proteins. [32] Like mtDNA, cpDNA is not fully autonomous and relies upon nuclear gene products for replication and production of chloroplast proteins. Plasmids usually carry at least one gene, and many of the genes that plasmids carry are beneficial to their host organisms. Theyare mainly found in bacteria, but also exist naturally in archaea and eukaryotes such as yeast and plants. Sentchilo V., Mayer A. P., Guy L., Miyazaki R., Green Tringe S., Barry K., et al.. (2013). ). Sekine M., Tanikawa S., Omata S., Saito M., Fujisawa T., Tsukatani N., et al.. (2006). The pheromone-responsive plasmids have mainly been described in Enterococcus faecalis. Vital component for expression vectors: determines which cell types the gene is expressed in and amount of recombinant protein obtained. have reported an in-depth investigation of Inc18 plasmids, which are found mostly in E. faecium (Rosvoll et al., 2010). Biology Dictionary. Construction of shuttle plasmids which can be efficiently mobilized from. carried out a plasmidome network analysis of all available complete bacterial plasmids to identify and characterize the most recent horizontal gene transfer or plasmid transfer (Yamashita et al., 2014). Soler N., Justome A., Quevillon-Cheruel S., Lorieux F., Le Cam E., Marguet E., et al.. (2007). The unclassified plasmids are shown as shaded, and the numbers of classified plasmids and unclassified plasmids are shown in parentheses (A). Allows for selection of plasmid-containing bacteria. (2005). Other examples include aberrant chromosomal fragments, such as double minute chromosomes, that can arise during artificial gene amplifications or in pathologic processes (e.g., cancer cell transformation). In addition to DNA found outside the nucleus in cells, infection by viral genomes also provides an example of extrachromosomal DNA. PCC 7120; Walton et al., 1992), pANS (pUH24) in Synechococus elongatus PCC 7942 (Golden and Sherman, 1983), pDC1 in Nostoc sp. There are multiple reviews of the conventional methods to detect plasmid transfer in various environments based on culture-dependent approaches (Smalla and Sobecky, 2002; Heuer and Smalla, 2007, 2012; Shintani et al., 2010). Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems, Sequence analysis of two cryptic plasmids from. As a library, NLM provides access to scientific literature. [18], Chromids are elements that exist at the boundary between a chromosome and a plasmid, found in about 10% of bacterial species sequenced by 2009. (2013). These linear plasmids require specialized mechanisms to replicate their ends. The term plasmid was introduced in 1952 by the American molecular biologist Joshua Lederberg to refer to "any extrachromosomal hereditary determinant. The average GC contents of plasmids in these groups were 48.0% in Gammaproteobacteria, 56.5% in Alphaproteobacteria, and 58.5% in Betaproteobacteria (Figure (Figure3A,3A, right). Addgene: Molecular Biology Reference Most plants inherit mtDNA maternally with one noted exception being the redwood Sequoia sempervirens that inherit mtDNA paternally. [23] Therefore, the reduction or complete elimination of extraneous noncoding backbone sequences would pointedly reduce the propensity for such events to take place, and consequently, the overall recombinogenic potential of the plasmid.[24][25]. Cloning vectors based on cryptic plasmids isolated from lactic acid bacteria: their characteristics and potential applications in biotechnology. Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate. compared the genomic structures of plasmids identified in four different Borrelia strains (Casjens et al., 2012). Pandza S., Biukovic G., Paravic A., Dadbin A., Cullum J., Hranueli D. (1998). The conformations are listed below in order of electrophoretic mobility (speed for a given applied voltage) from slowest to fastest: The rate of migration for small linear fragments is directly proportional to the voltage applied at low voltages. Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from. [33] In the context of eukaryotes, the term episome is used to mean a non-integrated extrachromosomal closed circular DNA molecule that may be replicated in the nucleus. Brown Kav A., Sasson G., Jami E., Doron-Faigenboim A., Benhar I., Mizrahi I. The majority of the 451 plasmids in Alphaproteobacteria were found in Rhizobiales (143 plasmids), Rhodospirillales (122 plasmids), Rhodobacteriales (94 plasmids), and Sphingomonadales (65 plasmids). The vector may also contain other marker genes or reporter genes to facilitate selection of plasmids with cloned inserts. Updates? Plasmid groups found in Enterobacteriales, such as Enterobacter, Escherichia, Salmonella, Shigella, and Yersinia, include a large number of virulence plasmids. Plasmids are physically separate from chromosomal DNA and replicate independently. The phylogenetic distribution of fully sequenced plasmids (A), histograms of plasmid size (B), and GC content (%) (C). ). Model organisms for genetics in the domain. Complete sequence of a 184-kilobase catabolic plasmid from. Dissemination of cephalosporin resistance genes between. They can be found in all three domains of microbes - archaea, bacteria, and eukarya/eukaryota. [26] These cloning vectors contain a site that allows DNA fragments to be inserted, for example a multiple cloning site or polylinker which has several commonly used restriction sites to which DNA fragments may be ligated. Physical mapping and characterization of a catabolic plasmid from the deep-subsurface bacterium. They are mostly found in bacteria. Considering that less than half of the plasmids in the database were able to be classified, there may still be unknown or novel types of plasmid replication or transfer systems in microbes. The classification will be also of help to predict host candidates of plasmids found by a metagenomics approach, rather than mostly a collection of results obtained. (1997). Different TLRs in human detect different PAMPS: lipopolysaccharides by TLR4, viral dsRNA by TLR3, viral ssRNA by TLR7/TLR8, viral or bacterial unmethylated DNA by TLR9. (2004). More than 90% of the plasmids in the database were identified in 22 phyla: Proteobacteria (2142 sequences, 47%), Firmicutes (1129 sequences, 25%), Spirochaetes (423 sequences, 9.2%), Actinobacteria (269 sequences, 5.8%), Cyanobacteria (136 sequences, 3.0%) Bacteroidetes (74 sequences, 1.6%), Chlamydiae (67 sequences, 1.5%), and Tenericutes (62 sequences, 1.3%; Figure Figure1A).1A). Although most plasmids are double-stranded DNA molecules, some consist of single-stranded DNA, or predominantly double-stranded RNA. Here, the Hok (Host-Killing) protein is not translated as long as the Sok antisense RNA is present. Finally, the overall productivity could be enhanced. [26], Eukaryotic chloroplasts, as well as the other plant plastids, also contain extrachromosomal DNA molecules. (2012). For this virus to persist, the circular genome must be replicated and inherited during cell division. [35] In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA. Plasmids naturally exist in bacterial cells, and they also occur in . RNA plasmids are non-infectious extrachromosomal linear RNA replicons, both encapsidated and unencapsidated, which have been found in fungi and various plants, from algae to land plants. The HPV DNA genome undergoes three distinct stages of replication: establishment, maintenance and amplification. Oliveira C. S., Moura A., Henriques I., Brown C. J., Rogers L. M., Top E. M., et al.. (2013). Many putative mobilizable plasmids were found in the phyla Proteobacteria (401/2141 plasmids, 18.7%), Firmicutes (285/1130 plasmids, 25.2%), Actinobacteria (64/269 plasmids, 23.8%), and Cyanobacteria (41/136 plasmids, 30.1%) (Figure (Figure2C).2C). Multiplex PCR as a tool for validating plasmid content of. Ravin recently reviewed the replication mechanisms of a prophage of Escherichia coli, N15, which was the first linear plasmid identified with covalently closed ends (Ravin, 2011). Sorvig E., Mathiesen G., Naterstad K., Eijsink V. G., Axelsson L. (2005). Shintani M., Matsui K., Inoue J., Hosoyama A., Ohji S., Yamazoe A., et al.. (2014a). Inc groups have been independently classified in three different genera; there are 27 Inc groups in Enterobacteriaceae, 14 Inc groups of Pseudomonas, and approximately 18 Inc groups in Staphylococcus (Udo and Grubb, 1991; Lawley et al., 2004; Taylor et al., 2004; Thomas and Haines, 2004; Sota and Top, 2008; Carattoli, 2009). Fluorescent cells are also detectable and separable with the use of flow cytometry or a micromanipulator at the single cell level; both methods have a strong potential to identify actual host ranges of plasmids (Musovic et al., 2010; Shintani et al., 2014a). [22] The number of mtDNA molecules per mitochondrion varies from species to species, as well as between cells with different energy demands. Several shuttle vectors are available for certain genera within Euryarcheoata, such as halophiles (Haloarcula), methanogens (Methaonococcus and Methonosarcina), and Thermococcales (Pyrococcus). (1993). Let us know if you have suggestions to improve this article (requires login). Plasmids are circular or linear extrachromosomal replicons that are found in many microorganisms in the domains Bacteria, Archaea, and Eukaryota (Funnell and Phillips, 2004). 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.[39][41]. Although plasmids containing these types of Rep genes have an average size of 484 kb, their sizes vary widely from 30 to 2430 kb (Figure (Figure3C3C). The majority of the lactic acid bacteria (LAB) that belong to Bacilli, including Lactococcus, Lactobacillus, Leuconostoc, Pediococcus, and Streptococcus, as well as Bifidobacterium (phylum Actinobacteria), are important in food fermentation. Some of the eukaryotes like yeast and plants also contain plasmids. are mainly found in bacteria, but also exist naturally in archaea and eukaryotes such as yeast and plants. Rep proteins of pKJ50, pNAC2, and pNAC3 were found only in Bifidobacterium; however, those of pDOJH10S were found in plasmids of other suborders of Actinobacteria, including Corynebacterineae, Micrococcinaea, and Propionibacterineae (Table S1). A plasmid that cannot be replicated B. Point mutations in or alternative gene arrangements of mtDNA have been linked to several diseases that affect the heart, central nervous system, endocrine system, gastrointestinal tract, eye, and kidney. Mutations in mtDNA or other cytoplasmic DNA will also be inherited from the mother. McLeod M. P., Warren R. L., Hsiao W. W., Araki N., Myhre M., Fernandes C., et al.. (2006). Casjens S., Palmer N., Van Vugt R., Huang W. M., Stevenson B., Rosa P., et al.. (2000). Notably, several circular plasmids in B31 are homologous throughout almost their entire lengths (cp32s) and carry many genes encoding lipoproteins located on cell surfaces, although very few of these are metabolic or housekeeping genes (Casjens et al., 2000). [22] The size of an animal mtDNA plasmid is roughly 16.6 kb and, although it contains genes for tRNA and mRNA synthesis, proteins coded for by nuclear genes are still required for the mtDNA to replicate or for mitochondrial proteins to be translated. In a review of the genomics of Actinobacteria, Ventura et al. Plasmid - an overview | ScienceDirect Topics [14] Once delivered into the host, the products of the plasmid genes will then stimulate both the innate immune response and the adaptive immune response of the host. [52][7][53], ecDNA is responsible for a large number of the more advanced and most serious cancers, as well as for the resistance to anti-cancer drugs.[54]. These linear plasmids have conserved telomeres containing inverted repeat sequences (Chen et al., 1993; Pandza et al., 1998). Genome stability of Lyme disease spirochetes: comparative genomics of. Indeed, plasmid transfer from Proteobacteria to Cyanobacteria has been previously reported (Encinas et al., 2014). 1 Answer Sorted by: 2 These resources may help. Stillwell L. C., Thurston S. J., Schneider R. P., Romine M. F., Fredrickson J. K., Saffer J. D. (1995). An increasing threat in hospitals: multidrug-resistant, The peptide pheromone-inducible conjugation system of. When this happens, a strain of bacteria can become resistant to antibiotics. [7][8][3] ecDNA is considered to be a primary mechanism of gene amplification, resulting in many copies of driver oncogenes and very aggressive cancers. Our editors will review what youve submitted and determine whether to revise the article. In molecular cloning, a plasmid is a type of vector. Le Dantec C., Winter N., Gicquel B., Vincent V., Picardeau M. (2001). She Q., Phan H., Garrett R. A., Albers S. V., Stedman K. M., Zillig W. (1998). The R. erythropolis PR4 strain is known to utilize n-alkanes and alkylbenzene, and it has three plasmids, pREL1, pREC1, and pREC2 (Sekine et al., 2006). Although vectors containing these origins could be a useful module to construct new vectors for Cyanobacteria, the homologous rep genes were not found in other plasmids in our database. A novel transformation of polychlorinated biphenyls by. Plasmids are the most-commonly used bacterial cloning vectors. Cyanobacteria are known for the ability to undergo oxygenic photosynthesis and are a promising platform for the production of renewable chemicals and fuels. (C) Histograms of plasmid size (left) and GC content (right) in phylum Actinobacteria. The plasmid DNA is similarly referred to as cloned DNA, and this process of generating multiple identical copies of a recombinant DNA molecule is known as DNA or molecular cloning. Huang C. H., Tsai H. H., Tsay Y. G., Chien Y. N., Wang S. L., Cheng M. Y., et al.. (2007). Plasmids are generally circular, but examples of linear plasmids are also known. Plasmids are small, circular pieces of DNA that are found in both prokaryotic and eukaryotic cells. Col plasmids contain genes that make bacteriocins (also known as colicins), which are proteins that kill other bacteria and thus defend the host bacterium. 14, 2020. Overview of DNA cloning DNA cloning is the process of making multiple, identical copies of a particular piece of DNA. Plasmid definition, a segment of DNA independent of the chromosomes and capable of replication, occurring in bacteria and yeast: used in recombinant DNA procedures to transfer genetic material from one cell to another. Cenciarini-Borde C., Courtois S., La Scola B. Several different plasmids have been found in E. coli. In this review, known plasmids for which the complete sequence was available were classified by their host and their (putative) replication or transfer systems. The best characterized plasmids among methanogens are pME2001, pURB500, and pC2A (Greve et al., 2004). The Supplementary Material for this article can be found online at: http://www.frontiersin.org/journal/10.3389/fmicb.2015.00242/abstract, National Library of Medicine Another class of plasmids, R factors, confers upon bacteria resistance to antibiotics. In contrast, plasmids used in biotechnology, such as pUC18, pBR322 and derived vectors, hardly ever contain toxin-antitoxin addiction systems, and therefore need to be kept under antibiotic pressure to avoid plasmid loss. The average sizes and GC contents of these plasmids varied widely (4631200,330 bp; 56.170.3%; Figures 5A,B). Plasmids are extremely valuable tools in the fields of molecular biology and genetics, specifically in the area of genetic engineering (q.v.). EcDNAs could be clustered together within the nucleus, which can be referred to as ecDNA hubs. They write new content and verify and edit content received from contributors. Notably, proteins responsible for replication initiation encoded on pCD-type plasmids showed high similarity with those encoded on IncZ plasmids, and 186 of the 976 plasmids of Enterobacteriales carried genes encoding these types of Rep proteins (Table S1). Plasmids Characteristics & Function | What are Plasmids? - Video Fertility F-plasmids B. DNA Plasmids C. Col Plasmids D. Virulence Plasmids, 2. This method enables researchers to search for plasmids in a wider microcosm containing the uncultivated microbial fraction (Heuer et al., 2012). There are difficulties with this method: (i) plasmids frequently carry multiple replicons, and it is therefore difficult to classify the plasmid into single replicon group. In a bacterium, different plasmids can only co-occur if they are compatible with each other. Most linear plasmids have conserved telomeres containing inverted repeat sequences (Ravin, 2011). Characteristics such as flexibility, versatility, safety, and cost-effectiveness enable molecular biologists to broadly utilize plasmids across a wide range of applications. The https:// ensures that you are connecting to the These plasmids are small, circular, double-stranded DNA structures naturally found in all bacterial cells. The mechanisms of replication control have been extensively studied in two iteron-containing plasmids, pPS10 and R6K (Giraldo and Fernandez-Tresguerres, 2004; Rakowski and Filutowicz, 2013). A plasmid is a small circular DNA molecule found in bacteria and some other microscopic organisms. Brown Kav A., Benhar I., Mizrahi I. 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. Table 4 lists the antibiotic resistances that have been found on plasmids in particular pathogenic organisms. These types of linear plasmids represent the largest class of extrachromosomal DNA as they are not only present in certain bacterial cells, but all linear extrachromosomal DNA molecules found in eukaryotic cells also take on this invertron structure with a protein attached to the 5 end. Jensen L. B., Garcia-Migura L., Valenzuela A. J., Lhr M., Hasman H., Aarestrup F. M. (2010a). The GC contents of both groups were similar, 32.3% and 34.1%, respectively (Figure (Figure4B,4B, right). Sometimes called EEs, extrachromosomal elements, have been associated with genomic instability in eukaryotes. Plasmid Definition & Meaning | Dictionary.com [27] To clone longer lengths of DNA, lambda phage with lysogeny genes deleted, cosmids, bacterial artificial chromosomes, or yeast artificial chromosomes are used. Conjugative type IV secretion systems in Gram-positive bacteria, A hybrid plasmid is a stable cloning vector for the cyanobacterium. The malaria parasite (genus Plasmodium), the AIDS-related pathogen (Taxoplasma and Cryptosporidium) are both members of the Apicomplexa group. Plasmids in Rhodococcus were found in the biphenyl degrader, R. jostii RHA1 (Seto et al., 1995). Inserting a plasmid into DNA would allow cells to express a protein that they are lacking. Horizontal gene transfer mediated by plasmids, Plasmids: Current Research and Future Trends. In humans, virtually all of the cytoplasm is inherited from the egg of the mother. Nagata Y., Natsui S., Endo R., Ohtsubo Y., Ichikawa N., Ankai A., et al.. (2011). Yeasts naturally harbour various plasmids. Mold, protozoan, and coelenterate mitochondrial, "Extrachromosomal oncogene amplification in tumour pathogenesis and evolution", "Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity", "Cancer May Be Driven by DNA Outside of Chromosomes", "Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA", "Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma", "Mitigating the looming vaccine crisis: production and delivery of plasmid-based vaccines", "Linear plasmids and chromosomes in bacteria", "Massive DNA 'Borg' structures perplex scientists", "Previously undiscovered DNA 'borgs' found on California wetlands", "Borgs are giant extrachromosomal elements with the potential to augment methane oxidation", "Quantitative evaluation of the mitochondrial DNA depletion syndrome", "Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms", "Rates and patterns of chloroplast DNA evolution", "Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants", "Circular chloroplast chromosomes: the grand illusion", "The loss of DNA from chloroplasts as leaves mature: fact or artefact? Their transfers are induced by pheromones generated from lipoprotein signal peptides encoded on the host chromosome (Clewell, 2007; Dunny, 2007). the contents by NLM or the National Institutes of Health. [5] The fact that this organelle contains its own DNA supports the hypothesis that mitochondria originated as bacterial cells engulfed by ancestral eukaryotic cells. Gene amplifications in cancer are often on extrachromosomal, circular elements. such as flexibility, versatility, safety, and cost-effectiveness enable molecular biologists to broadly utilize plasmids across a wide range of applications.