This single-stranded DNA is transferred into the recipient cell by the T4CP. Corrections? Fertility plasmids, also known as F-plasmids, contain transfer genes that allow genes to be transferred from one bacteria to another through conjugation. Plasmids are physically separate from chromosomal DNA and replicate independently. It is likely that plasmids with Rep types of pDOJH10S have a broad host range in the phylum Actinobacteria. Generally, scientists use plasmids to manipulate gene expression in target cells. Functional characterization of the origin of replication of pRN1 from, Plasmid rolling-circle replication: highlights of two decades of research. Complete sequence of a 184-kilobase catabolic plasmid from. But they can also be found in some yeasts, archaea, and plants. [10] Plasmids can also provide bacteria with the ability to fix nitrogen. Some of the eukaryotes like yeast and plants also contain plasmids. PCR using plasmid-specific sequences is one of the most common methods used to detect plasmids in environmental samples. Unlike other plasmids, F factor is constitutive for . compared the plasmid metagenomes from two separate activated sludge systems and found that the plasmids from the two environments were strongly different (Sentchilo et al., 2013). Plasmids are incompatible if they have the same reproduction strategy in the cell; this allows the plasmids to inhabit a certain territory within it without other plasmids interfering. Natural plasmids can be found in bacteria, archaea and eukaryotes, such as yeast and slime moulds [ 13 - 15 ]. (C) Histograms of plasmid size (left) and GC content (right) in phylum Actinobacteria. del Solar G., Moscoso M., Espinosa M. (1993). Complete genome sequence of the representative -hexachlorocyclohexane-degrading bacterium, Comparative analyses of base compositions, DNA sizes, and dinucleotide frequency profiles in archaeal and bacterial chromosomes and plasmids. Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in. Knowledge of the relationships between plasmid features and host taxonomy is important in order to understand how the plasmids have been spread among microbes. The two major peaks of mobilizable and transmissible plasmids were similarly found as those in previous report (Smillie et al., 2010). A plasmid that is attached to the cell membrane or integrated into the bacterial chromosome is called an episome (q.v.). Information about the host range of these plasmids is critical to effectively use them as genetic tools for microbial engineering. Unlike viruses, which encase their genetic material in a protective protein coat called a capsid, plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host; however, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer. Chen C. W., Yu T. W., Lin Y. S., Kieser H. M., Hopwood D. A. The classification lists in this review will be helpful to understand how these other genes on plasmids could be spread among microbes. Taylor D. E., Gibreel A., Lawley T. D., Tracz D. M. (2004). Generally, scientists use plasmids to manipulate gene expression in target cells. (2010) reported that about 14% of the full-sequenced plasmids were predicted to be . Several plasmids of the order Actinomycetales have conjugative systems that function in a manner similar to the segregation of chromosomal DNA during bacterial cell division and sporulation. Various primers and PCR methods to identify plasmids have been designed, such as those for Enterobacteriaceae (Carattoli et al., 2005), enterococci (Rosvoll et al., 2010), and other Gram-positive bacteria, mostly staphylococci (Clewell, 2007; Jensen et al., 2010a; Lozano et al., 2012). Only a small number of plasmids in Rhodococcus were predicted to have Rep proteins similar to those of pRHL1, pRHL3, pREC1, or pREC2 (Table S1). [34][35] Viruses are the most common examples of this, such as herpesviruses, adenoviruses, and polyomaviruses, but some are plasmids. Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria. The representative examples of these plasmids are pCF10 and pAD1 (Clewell, 2007; Dunny, 2007). D36 includes two cryptic plasmids and two carrying antibiotic resistance genes. Diverse broad-host-range plasmids from freshwater carry few accessory genes. Resistance or R plasmids contain genes that help a bacterial cell defend against environmental factors such as poisons or antibiotics. Plasmids naturally exist in bacterial cells, and they also occur in . Honeybees found to be less effective pollinators than native species. ", "A vector based on the SV40 origin of replication and chromosomal S/MARs replicates episomally in CHO cells", "The Hitchhiking principle: Optimizing episomal vectors for the use in gene therapy and biotechnology", "Replicating minicircles: Generation of nonviral episomes for the efficient modification of dividing cells", "Persistent episomal transgene expression in liver following delivery of a scaffold/matrix attachment region containing non-viral vector", "Strategies for the episomal modification of cells", "pEPito: a significantly improved non-viral episomal expression vector for mammalian cells", International Society for Plasmid Biology and other Mobile Genetic Elements, https://en.wikipedia.org/w/index.php?title=Plasmid&oldid=1159678565, Resistance (R) plasmids, which contain genes that provide resistance against, Col plasmids, which contain genes that code for. A. No use, distribution or reproduction is permitted which does not comply with these terms. Ratios of classified plasmids in each phylum (A) and histograms of their size (B, left) and GC content (B, right) are shown. A microbe can harbour different types of plasmids, but different plasmids can only exist in a single bacterial cell if they are compatible. Accessory regions pertaining to the bacterial backbone may engage in a wide range of structural instability phenomena. [10], 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. There are many ways to classify plasmids from general to specific. 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). Sen D., Van der Auwera G. A., Rogers L. M., Thomas C. M., Brown C. J., Top E. M. (2011). The IncP-1 plasmid is one of the best-studied plasmids distributed across many bacterial classes (Adamczyk and Jagura-Burdzy, 2003), and thus, its TrfA protein sequence was used to set the criteria for analysis. determined the complete sequence of pOZ176, an IncP-2 plasmid which is resistant to heavy metals (Xiong et al., 2013). Brolund A., Franzen O., Melefors O., Tegmark-Wisell K., Sandegren L. (2013). Additionally, plasmids are being investigated as a way to transfer genes into human cells as part of gene therapy. 0. . Although most plasmids are double-stranded DNA molecules, some consist of single-stranded DNA, or predominantly double-stranded RNA. The genetic element pSSVx of the extremely thermophilic crenarchaeon, Overview of the genetic tools in the Archaea. This is a cheap and easy way of mass-producing the protein the gene codes for, for example, insulin. Honeybees found to be less effective pollinators than native species. A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. Introduction Antimicrobial resistance (AMR), one of the biggest global threats to health and food safety, continues to be driven by misuse of antimicrobials in humans and animals. Therefore, characterizations of plasmid features involved in replication, maintenance, transfer, and host range based on molecular biological and biochemical methods are still necessary. Multiple plasmids can coexist in the same cell, each with different functions. Indeed, in our recent report of the whole genome sequence of a biphenyl-degrading bacterium, Geobacillus sp. The site is secure. Such events are frequently triggered by the transposition of mobile elements or by the presence of unstable elements such as non-canonical (non-B) structures. Of the 4602 plasmids included in our analysis, 388 plasmids could be classified using the 26 Rep families, and 383 of them were found in Firmicutes (Table S1). Cobley J. G., Zerweck E., Reyes R., Mody A., Seludo-Unson J. R., Jaeger H., et al.. (1993). A subset of 158 plasmids classified into Inc1 to Inc18 groups was found in Lactobacillales, including Enterococcus (36 plasmids), Lactobacilllus (56 plasmids), Lactococcus (15 plasmids), and Streptococcus (34 plasmids; Table S1). 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). Labidi A., David H. L., Roulland-Dussoix D. (1985). Encinas D., Garcillan-Barcia M. P., Santos-Merino M., Delaye L., Moya A., de la Cruz F. (2014). The plasmids have been generally classified into to two categories- circular and linear. In the case that one open reading frame simultaneously showed identity with the Rep proteins of these Inc groups, the one with the smaller e-value was used for the classification. Some plasmids contain genes called transfer genes that facilitate the beginning of conjugation. A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings, Single-cell identification in microbial communities by improved fluorescence, Horizontal gene exchange in environmental microbiota. Such single-copy plasmids have systems that attempt to actively distribute a copy to both daughter cells. If two plasmids are not compatible, one or the other will be rapidly lost from the cell. In either case, episomes remain physically separate from host cell chromosomes. This article has been posted to your Facebook page via Scitable LearnCast. They are mainly found in bacteria, but also exist naturally in archaea and eukaryotes such as yeast and plants. Accessibility Another classification system based on the nucleotide sequences of plasmids was proposed for enterococci and staphylococci, which included 26 Rep families and 10 unique families (Jensen et al., 2010a; Lozano et al., 2012). Plasmids in Rhodococcus were found in the biphenyl degrader, R. jostii RHA1 (Seto et al., 1995). Virulence Plasmids The plasmids from Enterobacteriales contain antibiotic resistance plasmids, which cause the rapid development of resistance to antibiotics in bacterial populations. Rosvoll T. C., Pedersen T., Sletvold H., Johnsen P. J., Sollid J. E., Simonsen G. S., et al.. (2010). However, this classification is not appropriate for non-transmissible plasmids. 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. [12], Plasmids almost always carry at least one gene. The Rep20 gene was also found in plasmids in Rhodospirillales and Rhodobacteriales (Figure (Figure3C).3C). Salmonella enterica is another bacterium that contains virulence plasmids. 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. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. There are five MPF types of plasmids, as defined by de la Cruz's group: (i) non-transmissible plasmids that do not code for a relaxase (non-mob); (ii) plasmids that do not contain a relaxase but contain T4CP, VirB4, and MPF, or any two of these three elements (non-mob, protein export); (iii) mobilizable plasmids that contain a relaxase gene but lack VirB4 and MPF (mob); (iv) conjugative plasmids that contain a known type of T4SS (MPFF, MPFT, MPFI or MPFG), plus relaxase and T4CP (determined conjugative); and (v) conjugative plasmids that contain genes for relaxase, T4CP, and VirB4, but whose T4SS does not belong to a specific MPF (undetermined conjugative). The parameters for identity and coverage were chosen based on variations in the amino acid sequences of the replication initiation protein TrfA from the IncP-1 plasmid (data not shown). Researchers also often upload plasmid sequences to the NCBI database, from which sequences of specific plasmids can be retrieved. Plasmids carry only a few genes and exist independently of chromosomes, the primary structures that contain DNA in cells. Plasmids within Proteobacteria are one of the most extensively studied groups because they include those harboring the pathogenic genes of bacteria known to infect both animals and plants. Plasmids are circular or linear extrachromosomal replicons that are found in many microorganisms in the domains Bacteria, Archaea, and Eukaryota (Funnell and Phillips, 2004 ). Many commercial kits have been created to perform plasmid extraction at various scales, purity, and levels of automation. The distribution of classified plasmids is shown in beige (pBL1 family), spring green (pCG1/pNG2 family), yellow (pMSC262 family), brown (plasmids with TapR1, TpgR1 Tac, and/or Tpc), light brown (pDOJH10S-type), and gray (IncP-1 plasmids), black (other Rep types), and white (unclassified plasmids). 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. Wide variations in both size and GC contents were observed among the 4602 plasmids found in the GenBank database. A. Regardless, once the cloning steps are complete, the vector containing the newly inserted gene is transformed into bacterial cells and selectively grown on antibiotic plates. They may be found as single or multiple copies and may carry from half a dozen to several hundred genes. Both pGT5 and pTN1 have been shown to use the rolling circle replication system (Arnold et al., 1999; Soler et al., 2007). Heuer H., Binh C. T., Jechalke S., Kopmann C., Zimmerling U., Krogerrecklenfort E., et al.. (2012). In cancers, these episomes passively replicate together with host chromosomes when the cell divides. (C) Histograms of plasmid size (left) and GC content (right) in Alphaproteobacteria. Straley S. C., Plano G. V., Skrzypek E., Haddix P. L., Fields K. A. This strain has three plasmids, pRHL1, pRHL2, and pRHL3 (Masai et al., 1997; Shimizu et al., 2001; McLeod et al., 2006). Currently, there are 4602 complete sequences of plasmids in the NCBI Plasmid Genome database: 4418 are from bacteria, 137 are from archaea, and the remaining 47 are from eukaryota (Figure (Figure1A;1A; based on the NCBI database, http://ftp.ncbi.nih.gov/genomes/Plasmids, Aug. 2014). 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. For example, the GC contents of the whole nucleotide sequences of 10 plasmids in Pseudomonas aeruginosa (Table S1) ranged from 45.8 to 63.8% (the average GC contents were 58.7%). Several types of plasmid addiction systems (toxin/ antitoxin, metabolism-based, ORT systems) were described in the literature[37] and used in biotechnical (fermentation) or biomedical (vaccine therapy) applications. Dealtry S., Holmsgaard P. N., Dunon V., Jechalke S., Ding G. C., Krogerrecklenfort E., et al.. (2014). plasmid / plasmids. A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches. Col plasmids: These plasmids contain genes that code for bacteriocins, proteins that can kill other bacteria. (1993). Control of ColE1 plasmid replication by antisense RNA. They can parasitize a conjugative plasmid, transferring at high frequency only in its presence. The majority of the 451 plasmids in Alphaproteobacteria were found in Rhizobiales (143 plasmids), Rhodospirillales (122 plasmids), Rhodobacteriales (94 plasmids), and Sphingomonadales (65 plasmids). [How does that work?] Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from. Jorgensen et al. 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). It replicates independently of chromosomal DNA. Crowley S., Bottacini F., Mahony J., van Sinderen D. (2013). The classification of plasmids into MOB classes and MPF types using T4CPs and VirB4 homologs was performed as proposed by de la Cruz's group (Garcilln-Barcia et al., 2009; Smillie et al., 2010). aeruginosa plasmids have been fully sequenced and analysed. This results in relatively large amounts (several hundred micrograms) of very pure plasmid DNA. Garcilln-Barcia et al. Molecular characterization of three plasmids from. The distribution of classified plasmids is shown in black (Inc1, Inc7, and Inc18), dark gray (Inc4, Inc8, Inc9, Inc10, Inc11, Inc13, and Inc14), light blue (Rep families number 124 containing 7b, 10b), light gray (other Inc or Rep types) and white (unclassified). 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). ", Biologydictionary.net Editors. When a virulence plasmid is inside a bacterium, it turns that bacterium into a pathogen, which is an agent of disease. Marine integrons containing novel integrase genes, attachment sites, attI, and associated gene cassettes in polluted sediments from Suez and Tokyo Bays. Drives transcription of the target gene. The notion of the episome", "Episomal vectors for gene expression in mammalian cells", "Transfer and expression of foreign genes in mammalian cells", "Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells", "Plasmid addiction systems: perspectives and applications in biotechnology", "Transformation of Saccharomyces cerevisiae with linear DNA killer plasmids from Kluyveromyces lactis", "The plant mitochondrial genome: Dynamics and maintenance", "Unique Features of the Mitochondrial Rolling Circle-Plasmid mp1 from the Higher Plant Chenopodium Album (L.)", "Linear plasmids in plant mitochondria: Peaceful coexistences or malicious invasions? plasmid, in microbiology, an extrachromosomal genetic element that occurs in many bacterial strains. Plasmid DNA may appear in one of five conformations, which (for a given size) run at different speeds in a gel during electrophoresis. Restriction digests are frequently used to analyse purified plasmids. Yamashita A., Sekizuka T., Kuroda M. (2014). 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). Identification of bacterial plasmids based on mobility and plasmid population biology. (2013). It is the first time this mechanism has been found in eukaryotes, such as animals. Indeed, about half of the plasmids in the database were found in Proteobacteria (Figure (Figure1A).1A). Michelle R. McGehee, in Molecular Biology (Third Edition), 2019 2.1 Plasmid Families and Incompatibility Two different plasmids that belong to the same family cannot co-exist in the same cell. PCC 7524 (Anabaena sp. 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 fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Key Terms. The majority of the plasmids within this phylum were found in the classes Gammaproteobacteria (1389; 63%), Alphaproteobacteria (451; 22%), and Betaproteobacteria (187; 8.7%). Plasmids 101 will provide you with an overview of general molecular biology knowledge and techniques, and empower you with a firm understanding of the fundamentals. In virulent Yersinia species, extensive research has been carried out on low calcium ion (Ca2+) response plasmids, which regulate the growth and expression of several virulence-associated properties by Ca2+ and temperature. Plasmids are circular or linear extrachromosomal replicons that are found in many microorganisms in the domains Bacteria, Archaea, and Eukaryota (Funnell and Phillips, 2004). There are five main classes: Plasmids can belong to more than one of these functional groups. The plasmids in Euryarcheoata had an average size of 119 kb and GC content of 52.1%, while those in Crenarchaeota were 20 kb and 39.2%, respectively. Thus, more than 75% of the plasmids in Enterobacteriales (697/927) were classified into Inc groups or Rep types, including IncF, IncA/C (equivalent to IncP-3), IncL/M, IncI, IncHI2/S, and IncN, containing plasmid families already known to carry resistance genes (Carattoli, 2009; Wang et al., 2013). 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). The features of Borrelia have been studied in detail (Chaconas and Kobryn, 2010; Chaconas and Norris, 2013). Molecular characterization of bla ESBL-harboring conjugative plasmids identified in multi-drug resistant. A plasmid is a small circular piece of DNA found in bacterial cells, and someone new to plasmids may need some extra guidance to understand the specific components that make up a plasmid and why each is important. The classification of plasmids based on their mobility (Garcilln-Barcia et al., 2009; Smillie et al., 2010; Garcilln-Barcia et al., 2011) can overcome these problems because (i) classification by MOB types can cover the whole microbial plasmids, and (ii) plasmids rarely carry more than one relaxase gene (Garcilln-Barcia et al., 2009). 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). Plasmids are the most-commonly used bacterial cloning vectors. Indeed, this method has been used to isolate a number of novel plasmids (Miyazaki et al., 2006; Sobecky and Hazen, 2009; Sen et al., 2011; Eikmeyer et al., 2012; Brown et al., 2013; Oliveira et al., 2013; Norberg et al., 2014). However, those specific to Crenarcheota are only useful for the genus Sulfolobales. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete. [22] Insertion sequences can also severely impact plasmid function and yield, by leading to deletions and rearrangements, activation, down-regulation or inactivation of neighboring gene expression. Edited by: Eva M. Top, University of Idaho, USA, Reviewed by: Itzhak Mizrahi, Agricultural Research Organization, Volcani Research Center, Israel; Claudia Oliveira, University of Aveiro, Portugal; Timothy J. Johnson, University of Minnesota, USA. All of the plasmids in the phylum Actinobacteria were found in class Actinobacteria, and, as shown in Figures 5A,B, they were found in nine suborders and one order (Bifidobacteriales). pSym contains the structural genes for nitrogenase (nifHDK) and/or genes essential to the production of the nodulation factor (notABC). [10], Plasmids may be present in an individual cell in varying number, ranging from one to several hundreds. 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. Plasmids are mainly found in bacteria, but they can also be found in archaea and multicellular organisms. plasmid is a small, circular, double-stranded DNA molecule that is distinct 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). The relationships between the phyla of plasmid hosts and plasmid size or GC content are shown in Figures 1B,C. Plasmids conferring resistance and virulence to Bacilli, including Enterococcus (Bacilliales) and Staphylococcus (Lactobacilliales), are causative agents of hospital infection outbreaks. The GC contents of both groups were similar, 32.3% and 34.1%, respectively (Figure (Figure4B,4B, right). (2011). The self-replicating unit, in this case, the plasmid, is called a replicon.
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