Plasmid: Definition, Structure, Vector, pBR322, Ti Plasmid - BYJU'S The average size of the 4602 plasmids (79.8 kb) was larger than those of 1730 plasmids (63.5 kb). For this virus to persist, the circular genome must be replicated and inherited during cell division. Metcalf W. W., Zhang J. K., Apolinario E., Sowers K. R., Wolfe R. S. (1997). Introduction of pSym into a plasmid-free A. tumefaciens strain leads to nodulation of a specific host and, sometimes, to nitrogen fixation, albeit at modest levels. F-plasmids are episomes, which are plasmids that can be inserted into chromosomal DNA. Degradative Plasmids 5. Based on the hypothesis, the relationships of GC contents between the plasmid and the host genome might be also important for predicting when the plasmid was introduced into the host species. Tilly et al. 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. These linear plasmids require specialized mechanisms to replicate their ends. This fact indicates that the distribution of plasmid sizes is conserved if the number of sequenced plasmids increases. Labidi A., David H. L., Roulland-Dussoix D. (1985). 3' to 5' exonuclease. EcDNAs could be clustered together within the nucleus, which can be referred to as ecDNA hubs. official website and that any information you provide is encrypted ATCC 29133; Lambert and Carr, 1983), and pFDA in Fremyella diplosiphon PCC 7601 (Cobley et al., 1993). Keywords Plasmids The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Michelle R. McGehee, in Molecular Biology (Third Edition), 2019 2 General Properties of Plasmids Plasmids are usually circular molecules of DNA, although occasionally, plasmids that are linear or made of RNA exist. Conjugative transfer is another important mechanism by which plasmids spread DNA among different bacteria. Importantly, because the bacteria from which plasmids are isolated grow quickly and make more of the plasmids as they grow, scientists can easily make large amounts of plasmid to manipulate and use in later work. The circular plasmids can replicate using the model of replication (as in Vicia faba) and through rolling circle replication (as in C.album). The difference was due to the number of plasmids more than 1 Mb in 4602 plasmids (45 plasmids) was much larger than those in 1730 plasmids (9 plasmids). Tauch A., Phler A., Kalinowski J., Thierbach G. (2003b). [27] To clone longer lengths of DNA, lambda phage with lysogeny genes deleted, cosmids, bacterial artificial chromosomes, or yeast artificial chromosomes are used. 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). [18][19][20], Mitochondria present in eukaryotic cells contain multiple copies of mitochondrial DNA (mtDNA) in the mitochondrial matrix. Thus, it was reasonable that plasmids found in Actinobacteria had the highest GC content (64.5%; Figure Figure1C),1C), because their host genomes ranged from 51% to greater than 70% GC (Ventura et al., 2007). This review will not consider plasmids of prokaryotic origin, even though certain bacterial plasmids, such as the tumor-inducing (Ti) plasmids of . Extrachromosomal DNA exists in prokaryotes outside the nucleoid region as circular or linear plasmids. Recently, Xiong et al. Brown C. J., Sen D., Yano H., Bauer M. L., Rogers L. M., Van der Auwera G. A., et al.. (2013). The ABCs of plasmid replication and segregation. Plasmids are important vehicles for the communication of genetic information between bacteria. This fact indicates that the size distribution of mobilizable and transmissible plasmids is conserved if the number of full-sequenced plasmids increases. The ecDNA chromatin architecture lacks the higher-order compaction that is present on chromosomal DNA and is among the most accessible DNA in the entire cancer genome. Arnold H. P., She Q., Phan H., Stedman K., Prangishvili D., Holz I., et al.. (1999). "[9] The term's early usage included any bacterial genetic material that exists extrachromosomally for at least part of its replication cycle, but because that description includes bacterial viruses, the notion of plasmid was refined over time to comprise genetic elements that reproduce autonomously. The genetic element pSSVx of the extremely thermophilic crenarchaeon, Overview of the genetic tools in the Archaea. Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome. Cloning vectors based on cryptic plasmids isolated from lactic acid bacteria: their characteristics and potential applications in biotechnology. Construction of shuttle plasmids which can be efficiently mobilized from. At higher voltages, larger fragments migrate at continuously increasing yet different rates. The average size was 80 kb (range: 744 bp-2.58 Mb), and the average GC content was 44.1% (range: 19.375.6%; Table S1). ecDNA are much larger than eccDNA, and are visible by light microscopy. While plasmids in the pBL1 family had small sizes (4.46.8 kb), those in the pCG1/pNG2 family had a wide range of sizes (4.185 kb, Figure Figure5C).5C). 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. Participating elements in the replication of iteron-containing plasmids. Degradative plasmids, which enable the digestion of unusual substances, e.g. Nishida reported that the GC contents of the majority of plasmids were lower than those of their host chromosomes, although the difference was less than 10% (Nishida, 2012). Extrachromosomal DNA in the cytoplasm has been found to be structurally different from nuclear DNA. (2010) reported that about 14% of the full-sequenced plasmids were predicted to be conjugative. Plasmids encoding ZFN could help deliver a therapeutic gene to a specific site so that cell damage, cancer-causing mutations, or an immune response is avoided.[28]. Acinetobacter baumannii is known to be an important pathogen, and the plasmids in the genus Acinetobacter are considered to be key genetic factors in the spread of multi-drug resistance (Dijkshoorn et al., 2007; Evans and Amyes, 2014). Discovery of a bacterium, with distinctive dioxygenase, that is responsible for, Pathogenomics of the virulence plasmids of, Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. The pNOB8-type plasmids are larger in size (around 30 kb) than pRN-type plasmids (less than 10 kb) and are known to be conjugative (She et al., 1998). Garcilln-Barcia et al. Plasmids have many different functions. No use, distribution or reproduction is permitted which does not comply with these terms. All About the Functions, Types, and Uses of Plasmids recently characterized the indispensable elements involved in the maintenance of cp26, a 26-kb circular plasmid found in B. burgdorferi (Tilly et al., 2012). They may be found as single or multiple copies and may carry from half a dozen to several hundred genes. Double minute chromosomes represent ~30% of the cancer-containing spectrum of ecDNA, including single bodies and have been found to contain identical gene content as single bodies. They suggested that there are at least 28 plasmid compatibility types among the four strains and that several inter-plasmid genomic rearrangements may have occurred. reported a novel approach for the reconstruction of mobile genetic elements from whole-genome sequence data, with which they discovered specific plasmid lineages shared between farm animals and humans (de Been et al., 2014). Park M. S., Shin D. W., Lee K. H., Ji G. E. (1999). The average size of these plasmids was 4.6 kb, while that of RepABC-type plasmids was 483 kb (Figure (Figure3C),3C), suggesting that the newly characterized Rep proteins may be appropriate for the replication of small plasmids. It will be therefore helpful for the classification to determine the nucleotide sequences of the other unsequenced Inc group plasmids including IncP-5, IncP-8, IncP-10, IncP-11, IncP-12, IncP-13, and IncP-14 plasmids (Table S2-1). Recently, the type bacterium that causes the sexually transmitted infection gonorrhea has become so resistant to a class of antibiotics called quinolones that a new class of antibiotics, called cephalosporins, has started to be recommended by the World Health Organization instead. [21] In multicellular animals, including humans, the circular mtDNA chromosome contains 13 genes that encode proteins that are part of the electron transport chain and 24 genes for Other mitochondrial proteins; these genes are broken down into 2 rRNA genes and 22 tRNA genes. Conjugation is one of the most effective mechanisms to spread genetic elements among bacteria (Guglielmini et al., 2011). Molecular characterization of bla ESBL-harboring conjugative plasmids identified in multi-drug resistant. Several different plasmids have been found in E. coli. Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria. 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). Restriction enzymes & DNA ligase (article) | Khan Academy A plasmid is a small circular DNA molecule found in bacteria and some other microscopic organisms. It is possible to purify certain fragments by cutting the bands out of the gel and dissolving the gel to release the DNA fragments. Although they have separate genes from their hosts, they are not considered to be independent life. Their antibiotic resistance genes, for example, prove useful in identifying those bacterial cells that have taken up the recombinant DNA molecule in a high background of untransformed cells (transformation frequencies are only about 1 out of every 100,000 cells). Another way to classify plasmids is by function. Ventura M., Canchaya C., Tauch A., Chandra G., Fitzgerald G. F., Chater K. F., et al.. (2007). Dealtry S., Holmsgaard P. N., Dunon V., Jechalke S., Ding G. C., Krogerrecklenfort E., et al.. (2014). It is theorized that the uniparental inheritance of mtDNA, which has a high mutation rate, might be a mechanism to maintain the homoplasmy of cytoplasmic DNA.[46]. Structure of 2 plasmid found in yeast. A team uncovers a surprising twist in the ways bacteria spread antibiotic-resistant genes. Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader. Inclusion in an NLM database does not imply endorsement of, or agreement with, The HPV DNA genome undergoes three distinct stages of replication: establishment, maintenance and amplification. Indeed, plasmid transfer from Proteobacteria to Cyanobacteria has been previously reported (Encinas et al., 2014). [10], Plasmids may be present in an individual cell in varying number, ranging from one to several hundreds. A short single-stranded DNA sequence used as an initiation point for PCR amplification or sequencing. The phylum Actinobacteria includes a wide variety of bacteria with different morphologies, physiologies, and metabolic properties, and they have various kinds of plasmids (Ventura et al., 2007). 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). Plasmids are so common in bacteria and archaea.. 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). [47], Extrachromosomal DNA is found in Apicomplexa, which is a group of protozoa. According to NPR, overuse of antibiotics to treat other infections, like urinary tract infections, may lead to the proliferation of drug-resistant strains. Plasmids are mainly found in bacteria, but they can also be found in archaea and multicellular organisms. In contrast, plasmids utilized in the lab are usually artificial and designed to introduce foreign DNA into another cell. Different plasmids may therefore be assigned to different incompatibility groups depending on whether they can coexist together. They typically have a small number of genes notably, some associated with antibiotic resistance and can be passed from one cell to another. This is a cheap and easy way of mass-producing the protein the gene codes for, for example, insulin. Halophiles are the Archaea living in the most saline environments on the earth, while Thermococcales are found in high temperature environments, mostly above 80C (Heuer and Smalla, 2012). Most known archaeal plasmids have cryptic phenotypes. determined the complete sequence of pOZ176, an IncP-2 plasmid which is resistant to heavy metals (Xiong et al., 2013). [34] In plants, eccDNA contain repeated sequences similar to those that are found in the centromeric regions of the chromosomes and in repetitive satellite DNA. Jorgensen T. S., Xu Z., Hansen M. A., Sorensen S. J., Hansen L. H. (2014). Plasmids are also important genetic tools used to manipulate and analyze microorganisms through the introduction, modification or removal of target genes (Frost et al., 2005; Sota and Top, 2008). Because C. glutamicum is widely used as an industrial producer of amino acids, plasmids of the amino acid-producing isolates were classified to develop efficient recombinant DNA techniques (Tauch et al., 2003a). The representative examples of these plasmids are pCF10 and pAD1 (Clewell, 2007; Dunny, 2007). Updates? Indeed, about half of the plasmids in the database were found in Proteobacteria (Figure (Figure1A).1A). This sits in the cytoplasm of the bacterial cell.. Self-transmissible plasmids in Gram-negative bacteria generally carry complete sets of genes required for transfer, the origin of transfer (oriT), the relaxase protein, the type IV coupling protein (T4CP), and the type IV secretion system (T4SS). The average sizes of plasmids in the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Euryarcheota were similarly distributed (6501200 kb), while those in Chlamydiae, Firmicutes, Spirocaetes, and Tenericutes were rather small (640 kb, Figure Figure1B).1B). Some of the many things that plasmids can be used to do include: Addgene has compiled various educational resources to facilitate plasmid use in the lab. [3] ecDNA are thought to be produced through double-strand breaks in chromosomes or over-replication of DNA in an organism. Each bacterium with a plasmid gives rise to a cluster of identical, plasmid-containing bacteria called a colony. This article is about the DNA molecule. Cevallos M. A., Cervantes-Rivera R., Gutierrez-Rios R. M. (2008). It is therefore one of the most important vehicles for bacterial communication of genetic information, facilitating the rapid evolution and adaptation abilities seen in bacteria (Aminov, 2011). They are double-stranded and self-replicating structures commonly found in various microorganisms, with bacteria being the most well-known hosts. Plasmids are small, circular pieces of DNA that are found in both prokaryotic and eukaryotic cells. Plasmid - an overview | ScienceDirect Topics Poehlein A., Kusian B., Friedrich B., Daniel R., Bowien B. A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. Horizontal gene transfer and the genomics of enterococcal antibiotic resistance. Plasmids are naturally occurring genetic elements found in microbial organisms. Greve B., Jensen S., Brgger K., Zillig W., Garrett R. A. At their most basic level, plasmids are small circular pieces of DNA that replicate independently from the host's chromosomal DNA. Song X., Sun J., Mikalsen T., Roberts A. P., Sundsfjord A. Two groups have recently reported the characterization of Rep proteins, Rep7 and Rep20, from small plasmids pGR7 (Grones and Grones, 2012) and pAG20 (Babic et al., 2014), respectively, found in Acetobacter (class Rhodospirillales). When the plasmid copies itself, it also makes copies of the inserted gene. Abstract Most plasmids are double-stranded circular DNA molecules. Fukaya M., Okumura H., Masai H., Uozumi T., Beppu T. (1985). Larger plasmids tend to have lower copy numbers. Characterisation of the plasmidome within. Huang C. H., Tsai H. H., Tsay Y. G., Chien Y. N., Wang S. L., Cheng M. Y., et al.. (2007). proposed PCR-based replicon typing of 19 groups (GRs) of resistance plasmids in A. baumannii on the basis of nucleotide sequence similarities between their replication initiation proteins (Bertini et al., 2010). Bacteria that cause disease can be easily spread and replicated among affected individuals. The local TBLASTN program was used for the classification of Rep proteins with the following parameters: e-value <105, >50% identity, and >0.5 query coverage. Nevertheless, a well-defined method for the classification of Acetobacter plasmids has not been developed. There are five main classes: Plasmids can belong to more than one of these functional groups. Genomic sequence of a Lyme disease spirochaete. Jeon C. O., Park W., Padmanabhan P., Derito C., Snape J. R., Madsen E. L. (2003). There were large differences in the average sizes and GC contents between the two phyla. Nagata Y., Ohtsubo Y., Endo R., Ichikawa N., Ankai A., Oguchi A., et al.. (2010). They are thought to be the products of gene rearrangements. Wang J., Stephan R., Karczmarczyk M., Yan Q., Hachler H., Fanning S. (2013). Although extrachromosomal circular DNA (eccDNA) is found in normal eukaryotic cells, extrachromosomal DNA (ecDNA) is a distinct entity that has been identified in the nuclei of cancer cells and has been shown to carry many copies of driver oncogenes. Bacterial DNA - a circular chromosome plus plasmids. A positive association between increased mtDNA levels and an increased risk for developing kidney tumors has been observed but there does not appear to be a link between mtDNA levels and the development of stomach cancer. Bacteria reproduce by sexual conjugation, which is the transfer of genetic material from one bacterial cell to another, either through direct contact or a bridge between the two cells. Novel assay to assess permissiveness of a soil microbial community toward receipt of mobile genetic elements. Characterization of pURB500 from the archaeon. 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. Some common plasmid types include cloning plasmids, If you have a question about a specific plasmid element that you would like answered or any topic suggestions for our, CRISPR Expression Systems and Delivery Methods, Plasmids 101: Green Fluorescent Protein (GFP), DNA sequence which allows initiation of replication within a plasmid by recruiting replication machinery proteins. Casjens et al. These DNA molecules have been researched as potential nucleotide target sites for antibiotics. The acetic acid bacteria are important for the industrial oxidation of various compounds, and thus, the construction of shuttle vector(s) to facilitate functional gene studies of these bacteria was reported 30 years ago (Fukaya et al., 1985; Okumura et al., 1985). Classification into an Inc group is always based on the amino acid sequence of the replication initiation (Rep) protein (replicon typing), and it is not necessarily confirmed by conventional methods whether the plasmid shows incompatibility with the same Inc group plasmid in the same host cell line. Addgene is a nonprofit plasmid repository. The average GC contents of plasmids classified into GR1-19 (38.4%) were lower than those of other plasmids in Gammaproteobacteria (Figure (Figure3B).3B). Most linear plasmids have conserved telomeres containing inverted repeat sequences (Ravin, 2011). Miyazaki R., Sato Y., Ito M., Ohtsubo Y., Nagata Y., Tsuda M. (2006). [citation needed], Plasmids of linear form are unknown among phytopathogens with one exception, Rhodococcus fascians.[14]. Bertini et al. A vector is a DNA sequence that can transport foreign genetic material from one cell to another cell, where the genes can be further expressed and replicated. In Vibrio cholerae, multiple type II toxin-antitoxin systems located in a super-integron were shown to prevent the loss of gene cassettes.. The average size of the pUT-type plasmids was 68.4 kb, which was larger than Rep20 type plasmids and smaller than RepABC-type plasmids (Figure (Figure3C).3C). 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). Hosts in the Rhizobiales are known to be symbiotic bacteria, and they can usually fix nitrogen only upon establishing a mutualistic interaction with plants, particularly those of the Leguminosae family (Cevallos et al., 2008; Pinto et al., 2012). Their sizes were relatively large (541797 kb, Figure Figure5C)5C) and their GC contents were high (68.371.9%, Figure Figure5C).5C). There are several methods to isolate plasmid DNA from bacteria, ranging from the miniprep to the maxiprep or bulkprep. Le Dantec C., Winter N., Gicquel B., Vincent V., Picardeau M. (2001). [46], There are two theories why the paternal mtDNA is rarely transmitted to the offspring. These findings suggest that plasmids from these Inc groups are closely related to one another. Chloroplasts contain multiple copies of cpDNA and the number can vary not only from species to species or cell type to cell type, but also within a single cell depending upon the age and stage of development of the cell. Although prokaryotic organisms do not possess a membrane-bound nucleus like eukaryotes, they do contain a nucleoid region in which the main chromosome is found. The GC contents of both groups were similar, 32.3% and 34.1%, respectively (Figure (Figure4B,4B, right). [21] The genes found on the cpDNA code for mRNAs that are responsible for producing necessary components of the photosynthetic pathway as well as coding for tRNAs, rRNAs, RNA polymerase subunits, and ribosomal protein subunits. Their 143 plasmids are characterized by a highly variable plasmid number (from 0 to 11) and size (from 150 to 1683 kb). Plasmids in Rhodococcus were found in the biphenyl degrader, R. jostii RHA1 (Seto et al., 1995). A few types of plasmids can also insert into the host chromosome, and these integrative plasmids are sometimes referred to as episomes in prokaryotes. Which is NOT one of the five main types of plasmids? This simplified figure depicts a bacteriums chromosomal DNA in red and plasmids in blue. Luo Y. R., Kang S. G., Kim S. J., Kim M. R., Li N., Lee J. H., et al.. (2012). The majority of plasmids in Gammaproteobacteria were from Enterobacteriales (927) and Pseudomonadales (183). It was suggested that the nucleotide composition of plasmid might be progressively altered toward the average nucleotide composition of the host genome (Lawrence and Ochman, 1998; Rocha and Danchin, 2002). These findings indicate that the plasmids with GR1- to GR19-type Rep proteins were primarily distributed in Acinetobacter and that GR3 group plasmids may have a broader host range than plasmids in other GR groups. E. coli is found naturally in the human gut and in other animals, but certain strains of E. coli can cause severe diarrhea and vomiting. Key Terms Col plasmids: These plasmids contain genes that code for bacteriocins, proteins that can kill other bacteria. Artificially constructed plasmids may be used as vectors in genetic engineering. These studies will not only enable us to understand the evolution of microbes mediated by plasmid transfers but will also provide us with useful tools for genetic analyses of both culturable and non-culturable microbes. plasmid, in microbiology, an extrachromosomal genetic element that occurs in many bacterial strains. [10] 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. Do All Bacteria Have Plasmids - Properties, Characteristics and Role Several Inc groups of Pseudomonas are identical to those in enterobacteria, such as IncP-1 (equivalent to IncP), IncP-3 (equivalent to IncA/C), IncP-4 (equivalent to IncQ), and IncP-6(equivalent to IncG/U). 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. [12] In the complex process of conjugation, plasmids may be transferred from one bacterium to another via sex pili encoded by some of the transfer genes (see figure). Toxin-antitoxin systems could prevent harmful large deletions in a bacterial genome, though arguably deletions of large coding regions are fatal to a daughter cell regardless. Transconjugants are selected by their phenotypes, such as antibiotic resistances, conferred by plasmid carriage. It is likely that plasmids with Rep types of pDOJH10S have a broad host range in the phylum Actinobacteria. (A) Histograms of plasmid size (left) and GC content (right) of Proteobacteria in each class. Some plasmids, however, have no observable effect on the phenotype of the host cell or its benefit to the host cells cannot be determined, and these plasmids are called cryptic plasmids. Our mission is to curate a one-stop reference guide for plasmids, so that you can spend less time researching the basics and spend more time developing cleverly designed experiments and innovative solutions necessary for advancing the field. This type of system was first found in plasmid R1. (1993). Bacteria containing the plasmid can then be grown in large amounts, harvested, and the plasmid of interest may then be isolated using various methods of plasmid preparation. Culture-independent methods to detect plasmids and their transfers are currently available for analyzing non-culturable or uncultivated microbes.
