Extrachromosomal DNA (abbreviated ecDNA) is any DNA that is found off the chromosomes , either inside or outside the nucleus of a cell . Most DNA in an individual genome is found in chromosomes contained in the nucleus. Multiple forms of extrachromosomal DNA exist, and, while some of these serve important biological functions, they can also play a role in diseases such as cancer.
103-456: A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria ; however, plasmids are sometimes present in archaea and eukaryotic organisms . Plasmids often carry useful genes, such as antibiotic resistance and virulence . While chromosomes are large and contain all
206-542: A hairpin loop or a covalently bonded protein attached to the telomeric ends of the DNA molecule. The adenine-thymine rich hairpin loops of the Borrelia bacteria range in size from 5 kilobase pairs (kb) to over 200 kb and contain the genes responsible for producing a group of major surface proteins, or antigens, on the bacteria that allow it to evade the immune response of its infected host. The linear plasmids which contain
309-767: A GEF, turning the GTPase on to create more GTP. It does not modify anything, but overdrives normal cellular internalization process, making it easier for the Bacteria to be colonized within a host cell. YopT ( Yersinia outer protein T) from Yersinia is an example of modification of the host. It modifies the proteolytic cleavage of carboxyl terminus of RhoA, releasing RhoA from the membrane. The mislocalization of RhoA causes downstream effectors to not work. A major category of virulence factors are bacterial toxins. These are divided into two groups: endotoxins and exotoxins . Endotoxin
412-691: A cell through multiple generations, but at some stage, they will exist as an independent plasmid molecule. 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. Viruses are the most common examples of this, such as herpesviruses , adenoviruses , and polyomaviruses , but some are plasmids. 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). Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that
515-417: 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 . 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 iterons , DnaA boxes, and an adjacent AT-rich region. Smaller plasmids make use of
618-1276: A copy of the plasmid survive, while a daughter cell that fails to inherit the plasmid dies or suffers a reduced growth-rate because of the lingering poison from the parent cell. Finally, the overall productivity could be enhanced. 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. Yeasts naturally harbour various plasmids. Notable among them are 2 μm plasmids—small circular plasmids often used for genetic engineering of yeast—and linear pGKL plasmids from Kluyveromyces lactis , that are responsible for killer phenotypes . Other types of plasmids are often related to yeast cloning vectors that include: The mitochondria of many higher plants contain self-replicating , extra-chromosomal linear or circular DNA molecules which have been considered to be plasmids. These can range from 0.7 kb to 20 kb in size. The plasmids have been generally classified into two categories- circular and linear. Circular plasmids have been isolated and found in many different plants, with those in Vicia faba and Chenopodium album being
721-465: A copy to both daughter cells. These systems, which include the parABS system and parMRC system , are often referred to as the partition system or partition function of a plasmid. Plasmids of linear form are unknown among phytopathogens with one exception, Rhodococcus fascians . Plasmids may be classified in a number of ways. Plasmids can be broadly classified into conjugative plasmids and non-conjugative plasmids. Conjugative plasmids contain
824-399: A few hundred kilobase (kb) segments, and contain an origin of replication which allows the plasmid to replicate independently of the bacterial chromosome. The total number of a particular plasmid within a cell is referred to as the copy number and can range from as few as two copies per cell to as many as several hundred copies per cell. Circular bacterial plasmids are classified according to
927-654: A filter to select only the bacteria containing the plasmid DNA. The vector may also contain other marker genes or reporter genes to facilitate selection of plasmids with cloned inserts. 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 . A plasmid cloning vector is typically used to clone DNA fragments of up to 15 kbp . To clone longer lengths of DNA, lambda phage with lysogeny genes deleted, cosmids , bacterial artificial chromosomes , or yeast artificial chromosomes are used. Another major use of plasmids
1030-420: A given size) run at different speeds in a gel during electrophoresis . 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. At higher voltages, larger fragments migrate at continuously increasing yet different rates. Thus,
1133-437: A high amount of LPS is present then septic shock (or endotoxic shock) may result which, in severe cases, can lead to death. As glycolipids (as opposed to peptides), endotoxins are not bound by B or T-cell receptors and do not elicit an adaptive immune response. Some bacteria secrete exotoxins, which have a wide range of effects, including inhibiting certain biochemical pathways in the host. The two most potent known exotoxins are
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#17327901060421236-420: A key role in anthrax pathogenesis. Exotoxins are extremely immunogenic and trigger the humoral response (antibodies target the toxin). Exotoxins are also produced by some fungi as a competitive resource. The toxins, named mycotoxins , deter other organisms from consuming the food the fungi colonise. As with bacterial toxins, there is a wide array of fungal toxins. Arguably one of the more dangerous mycotoxins
1339-452: A large number of commercially available cloning and expression vectors. 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 . Therefore, the reduction or complete elimination of extraneous noncoding backbone sequences would pointedly reduce the propensity for such events to take place, and consequently,
1442-588: A link between mtDNA levels and the development of stomach cancer . Extrachromosomal DNA is found in Apicomplexa , which is a group of protozoa . The malaria parasite (genus Plasmodium), the AIDS -related pathogen ( Taxoplasma and Cryptosporidium ) are both members of the Apicomplexa group. Mitochondrial DNA (mtDNA) was found in the malaria parasite. There are two forms of extrachromosomal DNA found in
1545-496: A major role in destruction of the pathogen through mechanisms such as opsonization . Some bacteria, such as Streptococcus pyogenes , are able to break down the host's immunoglobulins using proteases. Viruses also have notable virulence factors. Experimental research, for example, often focuses on creating environments that isolate and identify the role of " niche -specific virulence genes". These are genes that perform specific tasks within specific tissues/places at specific times;
1648-423: A mechanism to maintain the homoplasmy of cytoplasmic DNA. Sometimes called EEs, extrachromosomal elements, have been associated with genomic instability in eukaryotes. Small polydispersed DNAs (spcDNAs), a type of eccDNA, are commonly found in conjunction with genome instability. SpcDNAs are derived from repetitive sequences such as satellite DNA , retrovirus -like DNA elements, and transposable elements in
1751-644: A particular nutrient, including the ability to degrade recalcitrant or toxic organic compounds. Plasmids can also provide bacteria with the ability to fix nitrogen . Some plasmids, called cryptic plasmids , play a crucial role in horizontal genes transfer , since they carry antibiotic-resistance genes. Thus they are important factors in spreading resistance, which can result in antibiotic treatment failures. 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
1854-685: A paucity of repressive histone marks. 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. EcDNAs could be clustered together within the nucleus, which can be referred to as ecDNA hubs. Spacially, ecDNA hubs could cause intermolecular enhancer–gene interactions to promote oncogene overexpression. Virulence factor Virulence factors (preferably known as pathogenicity factors or effectors in botany ) are cellular structures, molecules and regulatory systems that enable microbial pathogens ( bacteria , viruses , fungi , and protozoa ) to achieve
1957-497: A plasmid containing the insulin gene leads to a large production of insulin. Plasmids may also be used for gene transfer as a potential treatment in gene therapy so that it may express the protein that is lacking in the cells. Some forms of gene therapy require the insertion of therapeutic genes at pre-selected chromosomal target sites within the human genome . Plasmid vectors are one of many approaches that could be used for this purpose. Zinc finger nucleases (ZFNs) offer
2060-411: A process called transformation . These plasmids contain a selectable marker , usually an antibiotic resistance gene, which confers on the bacteria an ability to survive and proliferate in a selective growth medium containing the particular antibiotics. The cells after transformation are exposed to the selective media, and only cells containing the plasmid may survive. In this way, the antibiotics act as
2163-400: A protein attached to the 5’ end. The long, linear " borgs " that co-occur with a species of archaeon – which may host them and shares many of their genes – could be an unknown form of extrachromosomal DNA structures. Mitochondria present in eukaryotic cells contain multiple copies of mitochondrial DNA (mtDNA) in the mitochondrial matrix . In multicellular animals, including humans,
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#17327901060422266-590: A protein that has been covalently attached to the 5’ end of the DNA strands are known as invertrons and can range in size from 9 kb to over 600 kb consisting of inverted terminal repeats . The linear plasmids with a covalently attached protein may assist with bacterial conjugation and integration of the plasmids into the genome. 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
2369-409: A range of proteases and lipases ; DNases , which break down DNA, and hemolysins which break down a variety of host cells, including red blood cells. A major group of virulence factors are proteins that can control the activation levels of GTPases . There are two ways in which they act. One is by acting as a GEF or GAP, and proceeding to look like a normally eukaryotic cellular protein. The other
2472-429: A role in the onset of disease in a variety of ways. 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. Loss of the amount of mtDNA present in the mitochondria can lead to a whole subset of diseases known as mitochondrial depletion syndromes (MDDs) which affect
2575-557: A selective advantage. ecDNA are much larger than eccDNA, and are visible by light microscopy. ecDNA in cancers generally range in size from 1-3 MB and beyond. Large ecDNA molecules have been found in the nuclei of human cancer cells and are shown to carry many copies of driver oncogenes , which are transcribed in tumor cells. Based on this evidence it is thought that ecDNA contributes to cancer growth. Specialized tools exist that allow ecDNA to be identified, such as Viral DNA are an example of extrachromosomal DNA. Understanding viral genomes
2678-519: A series of spontaneous events that culminate in an unforeseen rearrangement, loss, or gain of genetic material. 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. Accessory regions pertaining to the bacterial backbone may engage in a wide range of structural instability phenomena. Well-known catalysts of genetic instability include direct, inverted, and tandem repeats, which are known to be conspicuous in
2781-462: A set of transfer genes which promote sexual conjugation between different cells. 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). 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
2884-438: 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. 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
2987-421: A single ringed chromosome, however in some species there is evidence of multiple smaller ringed plasmids . 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. A single molecule of cpDNA can contain anywhere from 100 to 200 genes and varies in size from species to species. The size of cpDNA in higher plants
3090-440: A specific sequence, since they can easily be purified away from the rest of the genome. For their use as vectors, and for molecular cloning , plasmids often need to be isolated. There are several methods to isolate plasmid DNA from bacteria, ranging from the plasmid extraction kits ( miniprep to the maxiprep or bulkprep) , alkaline lysis , enzymatic lysis, and mechanical lysis . The former can be used to quickly find out whether
3193-424: A subset of the genes required for transfer. They can parasitize a conjugative plasmid, transferring at high frequency only in its presence. 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
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3296-424: A variety of substances such as aromatic compounds and xenobiotics . Bacterial plasmids can also function in pigment production, nitrogen fixation and the resistance to heavy metals. Naturally occurring circular plasmids can be modified to contain multiple resistance genes and several unique restriction sites , making them valuable tools as cloning vectors in biotechnology. Circular bacterial plasmids are also
3399-475: A way to cause a site-specific double-strand break to the DNA genome and cause homologous recombination . 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. Plasmids were historically used to genetically engineer the embryonic stem cells of rats to create rat genetic disease models. The limited efficiency of plasmid-based techniques precluded their use in
3502-553: A wide variety of other surface proteins to attach to host tissue. Capsules, made of carbohydrate, form part of the outer structure of many bacterial cells including Neisseria meningitidis . Capsules play important roles in immune evasion, as they inhibit phagocytosis , as well as protecting the bacteria while outside the host. Another group of virulence factors possessed by bacteria are immunoglobulin (Ig) proteases . Immunoglobulins are antibodies expressed and secreted by hosts in response to an infection. These immunoglobulins play
3605-706: Is aflatoxin produced by certain species of the genus Aspergillus (notably A. flavus ). If ingested repeatedly, this toxin can cause serious liver damage. Examples of virulence factors for Staphylococcus aureus are hyaluronidase , protease , coagulase , lipases , deoxyribonucleases and enterotoxins . Examples for Streptococcus pyogenes are M protein , lipoteichoic acid , hyaluronic acid capsule, destructive enzymes (including streptokinase , streptodornase , and hyaluronidase ), and exotoxins (including streptolysin ). Examples for Listeria monocytogenes include internalin A, internalin B, listeriolysin O , and actA, all of which are used to help colonize
3708-446: Is a component ( lipopolysaccharide (LPS) ) of the cell wall of gram-negative bacteria. It is the lipid A part of this LPS which is toxic. Lipid A is an endotoxin. Endotoxins trigger intense inflammation. They bind to receptors on monocytes causing the release of inflammatory mediators which induce degranulation . As part of this immune response cytokines are released; these can cause the fever and other symptoms seen during disease. If
3811-443: Is around 120–160 kb. 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. Like mtDNA, cpDNA is not fully autonomous and relies upon nuclear gene products for replication and production of chloroplast proteins. Chloroplasts contain multiple copies of cpDNA and
3914-506: Is covalently modifying the GTPase itself. The first way is reversible; many bacteria like Salmonella have two proteins to turn the GTPases on and off. The other process is irreversible, using toxins to completely change the target GTPase and shut down or override gene expression. One example of a bacterial virulence factor acting like a eukaryotic protein is Salmonella protein SopE it acts as
4017-432: Is demonstrated by using a suitable host that can mass produce specialized metabolites, some of these molecules are able to control microbial population. Plasmids can contain and express several BGCs with a few plasmids known to be exclusive for transferring BGCs. BGC's can also be transfers to the host organism's chromosome, utilizing a plasmid vector, which allows for studies in gene knockout experiments. By using plasmids for
4120-471: Is easy to identify and isolate. 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 . ecDNA is considered to be a primary mechanism of gene amplification , resulting in many copies of driver oncogenes and very aggressive cancers. Extrachromosomal DNA in
4223-438: Is normally inserted into a plasmid that typically contains a number of features for their use. These include a gene that confers resistance to particular antibiotics ( ampicillin is most frequently used for bacterial strains), an origin of replication to allow the bacterial cells to replicate the plasmid DNA, and a suitable site for cloning (referred to as a multiple cloning site ). DNA structural instability can be defined as
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4326-474: Is one mechanism of horizontal gene transfer , and plasmids are considered part of the mobilome . 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. Plasmids vary in size from 1 to over 400 k bp , and
4429-423: Is possible to transfer the a clone of the DNA from Yersinia to a non-pathogenic E. coli and have them express the pathogenic virulence factor. Transposon , a DNA element inserted at random, mutagenesis of bacteria DNA is also a highly used experimental technique done by scientists. These transposons carry a marker that can be identified within the DNA. When placed at random, the transposon may be placed next to
4532-438: Is primarily found in plasmids , whereas, in eukaryotes extrachromosomal DNA is primarily found in organelles . Mitochondrial DNA is a main source of this extrachromosomal DNA in eukaryotes. The fact that this organelle contains its own DNA supports the hypothesis that mitochondria originated as bacterial cells engulfed by ancestral eukaryotic cells. Extrachromosomal DNA is often used in research into replication because it
4635-545: Is responsible for a large number of the more advanced and most serious cancers, as well as for the resistance to anti-cancer drugs. The circular shape of ecDNA differs from the linear structure of chromosomal DNA in meaningful ways that influence cancer pathogenesis . Oncogenes encoded on ecDNA have massive transcriptional output, ranking in the top 1% of genes in the entire transcriptome . In contrast to bacterial plasmids or mitochondrial DNA, ecDNA are chromatinized, containing high levels of active histone marks, but
4738-608: Is supported by bioinformatics software . These programs record the DNA sequence of plasmid vectors, help to predict cut sites of restriction enzymes , and to plan manipulations. Examples of software packages that handle plasmid maps are ApE, Clone Manager , GeneConstructionKit, Geneious, Genome Compiler , LabGenius, Lasergene, MacVector , pDraw32, Serial Cloner, UGENE , VectorFriends, Vector NTI , and WebDSV. These pieces of software help conduct entire experiments in silico before doing wet experiments. Many plasmids have been created over
4841-521: Is the human papillomavirus ( HPV ). The HPV DNA genome undergoes three distinct stages of replication: establishment, maintenance and amplification. HPV infects epithelial cells in the anogenital tract and oral cavity. Normally, HPV is detected and cleared by the immune system. The recognition of viral DNA is an important part of immune responses. For this virus to persist, the circular genome must be replicated and inherited during cell division. Cells can recognize foreign cytoplasmic DNA. Understanding
4944-422: Is to enable the tumor to rapidly reach high copy numbers , while also promoting rapid, massive cell-to-cell genetic heterogeneity . The most commonly amplified oncogenes in cancer are found on ecDNA and have been shown to be highly dynamic, re-integrating into non-native chromosomes as homogeneous staining regions (HSRs) and altering copy numbers and composition in response to various drug treatments. ecDNA
5047-412: Is to make large amounts of proteins. In this case, researchers grow bacteria containing a plasmid harboring the gene of interest. Just as the bacterium produces proteins to confer its antibiotic resistance, it can also be induced to produce large amounts of proteins from the inserted gene. This is a cheap and easy way of mass-producing the protein, for example, utilizing the rapid reproduction of E.coli with
5150-412: Is very important for understanding the evolution and mutation of the virus. Some viruses, such as HIV and oncogenic viruses , incorporate their own DNA into the genome of the host cell. Viral genomes can be made up of single stranded DNA ( ssDNA ), double stranded DNA ( dsDNA ) and can be found in both linear and circular form. One example of infection of a virus constituting as extrachromosomal DNA
5253-411: The centromeric regions of the chromosomes and in repetitive satellite DNA. In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA , 5S ribosomal DNA and telomere DNA. Certain organisms, such as yeast, rely on chromosomal DNA replication to produce eccDNA whereas eccDNA formation can occur in other organisms, such as mammals, independently of
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#17327901060425356-403: The cytoplasm has been found to be structurally different from nuclear DNA. Cytoplasmic DNA is less methylated than DNA found within the nucleus. It was also confirmed that the sequences of cytoplasmic DNA were different from nuclear DNA in the same organism, showing that cytoplasmic DNAs are not simply fragments of nuclear DNA. In cancer cells, ecDNA have been shown to be primarily isolated to
5459-474: The hok/sok (host killing/suppressor of killing) system of plasmid R1 in Escherichia coli . This variant produces both a long-lived poison and a short-lived antidote . Several types of plasmid addiction systems (toxin/ antitoxin, metabolism-based, ORT systems) were described in the literature and used in biotechnical (fermentation) or biomedical (vaccine therapy) applications. Daughter cells that retain
5562-525: The 3-base sequences (codons) in the mtDNA of these organisms do code for the same amino acids as those of the nuclear genetic code, a few are different. The coding differences are thought to be a result of chemical modifications in the transfer RNAs that interact with the messenger RNAs produced as a result of transcribing the mtDNA sequences. Eukaryotic chloroplasts , as well as the other plant plastids , also contain extrachromosomal DNA molecules. Most chloroplasts house all of their genetic material in
5665-416: The DNA at certain short sequences. The resulting linear fragments form 'bands' after gel electrophoresis . It is possible to purify certain fragments by cutting the bands out of the gel and dissolving the gel to release the DNA fragments. Because of its tight conformation, supercoiled DNA migrates faster through a gel than linear or open-circular DNA. The use of plasmids as a technique in molecular biology
5768-624: The DNA is stably maintained and replicated with the host cell. Cytoplasmic viral episomes (as in poxvirus infections) can also occur. Some episomes, such as herpesviruses, replicate in a rolling circle mechanism, similar to bacteriophages (bacterial phage viruses). Others replicate through a bidirectional replication mechanism ( Theta type plasmids). In either case, episomes remain physically separate from host cell chromosomes. Several cancer viruses, including Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus , are maintained as latent, chromosomally distinct episomes in cancer cells, where
5871-485: The bacterial virulence factors. Bacterial DNA can be altered from pathogenic to non-pathogenic, random mutations may be introduced to their genome, specific genes encoding for membrane or secretory products may be identified and mutated, and genes that regulate virulence genes maybe identified. Experiments involving Yersinia pseudotuberculosis have been used to change the virulence phenotype of non-pathogenic bacteria to pathogenic. Because of horizontal gene transfer, it
5974-476: The basis for the production of DNA vaccines . Plasmid DNA vaccines are genetically engineered to contain a gene which encodes for an antigen or a protein produced by a pathogenic virus, bacterium or other parasites. 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. The plasmids are often coated with some type of adjuvant prior to delivery to enhance
6077-411: 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. In Vibrio , the bacterium synchronizes
6180-970: 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. Another way to classify plasmids is by function. There are five main classes: Plasmids can belong to more than one of these functional groups. 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 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. Chromids are elements that exist at
6283-399: The circular mtDNA chromosome contains 13 genes that encode proteins that are part of the electron transport chain and 24 genes for mitochondrial RNAs; these genes are broken down into 2 rRNA genes and 22 tRNA genes. 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
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#17327901060426386-560: The circular plasmids share a common ancestor, some genes in the mitochondrial plasmid have counterparts in the nuclear DNA suggesting inter-compartment exchange. 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. Plasmids are often used to purify
6489-488: The creation of more accurate human cell models. However, developments in adeno-associated virus recombination techniques, and zinc finger nucleases , have enabled the creation of a new generation of isogenic human disease models . Plasmids assist in transporting biogenetic gene clusters - a set of gene that contain all the necessary enzymes that lead to the production of special metabolites (formally known as secondary metabolite) . A benefit of using plasmids to transfer BGC
6592-492: The damaged mtDNA molecule is destroyed (without causing damage to the mitochondrion since there are multiple copies of mtDNA per mitochondrion). The standard genetic code by which nuclear genes are translated is universal, meaning that each 3-base sequence of DNA codes for the same amino acid regardless of what species from which the DNA comes. However, this code is quite universal and is slightly different in mitochondrial DNA of fungi, animals, protists and plants. While most of
6695-480: The egg of the mother. For this reason, organelle DNA, including mtDNA, is inherited from the mother. Mutations in mtDNA or other cytoplasmic DNA will also be inherited from the mother. This uniparental inheritance is an example of non-Mendelian inheritance . Plants also show uniparental mtDNA inheritance. Most plants inherit mtDNA maternally with one noted exception being the redwood Sequoia sempervirens that inherit mtDNA paternally. There are two theories why
6798-456: The essential genetic information for living under normal conditions, plasmids are usually very small and contain additional genes for special circumstances. Artificial plasmids are widely used as vectors in molecular cloning , serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation . Synthetic plasmids are available for procurement over
6901-501: The following: Specific pathogens possess a wide array of virulence factors. Some are chromosomally encoded and intrinsic to the bacteria (e.g. capsules and endotoxin ), whereas others are obtained from mobile genetic elements like plasmids and bacteriophages (e.g. some exotoxins). Virulence factors encoded on mobile genetic elements spread through horizontal gene transfer , and can convert harmless bacteria into dangerous pathogens. Bacteria like Escherichia coli O157:H7 gain
7004-467: The genes encoding them have been proposed. Small molecules being investigated for their ability to inhibit virulence factors and virulence factor expression include alkaloids , flavonoids , and peptides . Experimental studies are done to characterize specific bacterial pathogens and to identify their specific virulence factors. Scientists are trying to better understand these virulence factors through identification and analysis to better understand
7107-489: The genome. They are thought to be the products of gene rearrangements. Extrachromosomal DNA ( ecDNA ) found in cancer have historically been referred to as Double minute chromosomes (DMs), which present as paired chromatin bodies under light microscopy . 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. The ecDNA notation encompasses all forms of
7210-416: 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 factors that enable a bacterium to colonize a host and overcome its defences or have specific metabolic functions that allow the bacterium to utilize
7313-409: 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 episomes in prokaryotes . Plasmids almost always carry at least one gene. Many of the genes carried by a plasmid are beneficial for
7416-477: The host. Examples for Yersinia pestis are an altered form of lipopolysaccharide, type three secretion system, and YopE and YopJ pathogenicity. The cytolytic peptide Candidalysin is produced during hyphal formation by Candida albicans ; it is an example of a virulence factor from a fungus. Other virulence factors include factors required for biofilm formation (e.g. sortases ) and integrins (e.g. beta-1 and 3). Strategies to target virulence factors and
7519-472: The immune response from the host. Linear bacterial plasmids have been identified in several species of spirochete bacteria , including members of the genus Borrelia (to which the pathogen responsible for Lyme disease belongs), several species of the gram positive soil bacteria of the genus Streptomyces , and in the gram negative species Thiobacillus versutus , a bacterium that oxidizes sulfur. Linear plasmids of prokaryotes are found either containing
7622-408: The infectious process in hopes that new diagnostic techniques, specific antimicrobial compounds, and effective vaccines or toxoids may be eventually produced to treat and prevent infection. There are three general experimental ways for the virulence factors to be identified: biochemically, immunologically, and genetically. For the most part, the genetic approach is the most extensive way in identifying
7725-522: The internet by various vendors using submitted sequences typically designed with software, if a design does not work the vendor may make additional edits from the submission. Plasmids are considered replicons , units of DNA capable of replicating autonomously within a suitable host. However, plasmids, like viruses , are not generally classified as life . Plasmids are transmitted from one bacterium to another (even of another species) mostly through conjugation . This host-to-host transfer of genetic material
7828-455: The large, oncogene-containing, extrachromosomal DNA found in cancer cells. This type of ecDNA is commonly seen in cancer cells of various histologies, but virtually never in normal cells. ecDNA are thought to be produced through double-strand breaks in chromosomes or over-replication of DNA in an organism. Studies show that in cases of cancer and other genomic instability, higher levels of EEs can be observed. Mitochondrial DNA can play
7931-559: The liver, central and peripheral nervous systems, smooth muscle and hearing in humans. There have been mixed, and sometimes conflicting, results in studies that attempt to link mtDNA copy number to the risk of developing certain cancers. Studies have been conducted that show an association between both increased and decreased mtDNA levels and the increased risk of developing breast cancer . 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
8034-634: The majority of their virulence from mobile genetic elements. Gram-negative bacteria secrete a variety of virulence factors at host–pathogen interface , via membrane vesicle trafficking as bacterial outer membrane vesicles for invasion, nutrition and other cell-cell communications. It has been found that many pathogens have converged on similar virulence factors to battle against eukaryotic host defenses. These obtained bacterial virulence factors have two different routes used to help them survive and grow: Bacteria produce various adhesins including lipoteichoic acid , trimeric autotransporter adhesins and
8137-410: The malaria parasites. One of these is 6-kb linear DNA and the second is 35-kb circular DNA. These DNA molecules have been researched as potential nucleotide target sites for antibiotics . Gene amplification is among the most common mechanisms of oncogene activation. Gene amplifications in cancer are often on extrachromosomal, circular elements. One of the primary functions of ecDNA in cancer
8240-529: The most studied and whose mechanism of replication is known. The circular plasmids can replicate using the θ model of replication (as in Vicia faba ) and through rolling circle replication (as in C.album ). Linear plasmids have been identified in some plant species such as Beta vulgaris , Brassica napus , Zea mays , etc. but are rarer than their circular counterparts. The function and origin of these plasmids remains largely unknown. It has been suggested that
8343-560: The mtDNA to replicate or for mitochondrial proteins to be translated. There is only one region of the mitochondrial chromosome that does not contain a coding sequence, the 1 kb region known as the D-loop to which nuclear regulatory proteins bind. The number of mtDNA molecules per mitochondrion varies from species to species, as well as between cells with different energy demands. For example, muscle and liver cells contain more copies of mtDNA per mitochondrion than blood and skin cells do. Due to
8446-533: The notion of plasmid was refined over time to refer to genetic elements that reproduce autonomously. Later in 1968, it was decided that the term plasmid should be adopted as the term for extrachromosomal genetic element, and to distinguish it from viruses, the definition was narrowed to genetic elements that exist exclusively or predominantly outside of the chromosome, can replicate autonomously, and contribute to transferring mobile elements between unrelated bacteria. In order for plasmids to replicate independently within
8549-501: The nucleus (reviewed in ). In addition to DNA found outside the nucleus in cells, infection by viral genomes also provides an example of extrachromosomal DNA. 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. Extrachromosomal DNA exists in prokaryotes outside the nucleoid region as circular or linear plasmids . Bacterial plasmids are typically short sequences, consisting of 1 to
8652-837: 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. For example, cpDNA content in the chloroplasts of young cells, during the early stages of development where the chloroplasts are in the form of indistinct proplastids, are much higher than those present when that cell matures and expands, containing fully mature plastids. Extrachromosomal circular DNA (eccDNA) are present in all eukaryotic cells , are usually derived from genomic DNA, and consist of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 base pairs to more than 20,000 base pairs. In plants, eccDNA contain repeated sequences similar to those that are found in
8755-494: The number of identical plasmids in a single cell can range from one up to thousands. The term plasmid was coined in 1952 by the American molecular biologist Joshua Lederberg to refer to "any extrachromosomal hereditary determinant." 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,
8858-426: The overall recombinogenic potential of the plasmid. Plasmids are the most-commonly used bacterial cloning vectors. 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 . After the gene of interest is inserted, the plasmids are introduced into bacteria by
8961-414: The paternal mtDNA is rarely transmitted to the offspring. One is simply the fact that paternal mtDNA is at such a lower concentration than the maternal mtDNA and thus it is not detectable in the offspring. A second, more complex theory, involves the digestion of the paternal mtDNA to prevent its inheritance. It is theorized that the uniparental inheritance of mtDNA, which has a high mutation rate , might be
9064-675: The plasmid is correct in any of several bacterial clones. The yield is a small amount of impure plasmid DNA, which is sufficient for analysis by restriction digest and for some cloning techniques. In the latter, much larger volumes of bacterial suspension are grown from which a maxi-prep can be performed. In essence, this is a scaled-up miniprep followed by additional purification. This results in relatively large amounts (several hundred micrograms) of very pure plasmid DNA. Many commercial kits have been created to perform plasmid extraction at various scales, purity, and levels of automation. Plasmid DNA may appear in one of five conformations, which (for
9167-494: The preferred term for autonomously replicating extrachromosomal DNA. At a 1968 symposium in London some participants suggested that the term episome be abandoned, although others continued to use the term with a shift in meaning. Today, some authors use episome in the context of prokaryotes to refer to a plasmid that is capable of integrating into the chromosome. The integrative plasmids may be replicated and stably maintained in
9270-404: The production of IFN (type I interferons ) and other cytokines . Inheritance of extrachromosomal DNA differs from the inheritance of nuclear DNA found in chromosomes. Unlike chromosomes, ecDNA does not contain centromeres and therefore exhibits a non-Mendelian inheritance pattern that gives rise to heterogeneous cell populations. In humans, virtually all of the cytoplasm is inherited from
9373-402: The proximity of the electron transport chain within the mitochondrial inner membrane and the production of reactive oxygen species (ROS), and due to the fact that the mtDNA molecule is not bound by or protected by histones, the mtDNA is more susceptible to DNA damage than nuclear DNA. In cases where mtDNA damage does occur, the DNA can either be repaired via base excision repair pathways, or
9476-897: The recognition pathways has implications towards prevention and treatment of diseases. Cells have sensors that can specifically recognize viral DNA such as the Toll-like receptor (TLR) pathway. The Toll Pathway was recognized, first in insects, as a pathway that allows certain cell types to act as sensors capable of detecting a variety of bacterial or viral genomes and PAMPS ( pathogen-associated molecular patterns ). PAMPs are known to be potent activators of innate immune signaling. There are approximately 10 human Toll-Like Receptors (TLRs). 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 . TLR9 has evolved to detect CpG DNA commonly found in bacteria and viruses and to initiate
9579-441: The replication of the chromosome and chromid by a conserved genome size ratio. Artificially constructed plasmids may be used as vectors in genetic engineering . These plasmids serve as important tools in genetics and biotechnology labs, where they are commonly used to clone and amplify (make many copies of) or express particular genes. A wide variety of plasmids are commercially available for such uses. The gene to be replicated
9682-474: The replication process. The function of eccDNA have not been widely studied, but it has been proposed that the production of eccDNA elements from genomic DNA sequences add to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes. A distinct type of extrachromosomal DNA, denoted as ecDNA, is commonly observed in human cancer cells. ecDNA found in cancer cells contain one or more genes that confer
9785-493: The resolution of a gel decreases with increased voltage. At a specified, low voltage, the migration rate of small linear DNA fragments is a function of their length. Large linear fragments (over 20 kb or so) migrate at a certain fixed rate regardless of length. This is because the molecules 'respirate', with the bulk of the molecule following the leading end through the gel matrix. Restriction digests are frequently used to analyse purified plasmids. These enzymes specifically break
9888-458: The special functions that the genes encoded on the plasmid provide. Fertility plasmids, or f plasmids, allow for conjugation to occur whereas resistance plasmids, or r plasmids, contain genes that convey resistance to a variety of different antibiotics such as ampicillin and tetracycline. Virulence plasmids contain the genetic elements necessary for bacteria to become pathogenic. Degradative plasmids that contain genes that allow bacteria to degrade
9991-424: The sum total of niche-specific genes is the virus' virulence . Genes characteristic of this concept are those that control latency in some viruses like herpes. Murine gamma herpesvirus 68 (γHV68) and human herpesviruses depend on a subset of genes that allow them to maintain a chronic infection by reactivating when specific environmental conditions are met. Even though they are not essential for lytic phases of
10094-563: The tetanus toxin ( tetanospasmin ) secreted by Clostridium tetani and the botulinum toxin secreted by Clostridium botulinum . Exotoxins are also produced by a range of other bacteria including Escherichia coli ; Vibrio cholerae (causative agent of cholera ); Clostridium perfringens (common causative agent of food poisoning as well as gas gangrene ) and Clostridioides difficile (causative agent of pseudomembranous colitis ). A potent three-protein virulence factor produced by Bacillus anthracis , called anthrax toxin , plays
10197-401: 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. 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
10300-460: The uptake of BGCs, microorganisms can gain an advantage as production is not limited to antibiotic resistant biosynthesis genes but the production of toxin s/antitoxins. The term episome was introduced by François Jacob and Élie Wollman in 1958 to refer to extra-chromosomal genetic material that may replicate autonomously or become integrated into the chromosome. Since the term was introduced, however, its use has changed, as plasmid has become
10403-410: The virus, these latency genes are important for promoting chronic infection and continued replication within infected individuals. Some bacteria, such as Streptococcus pyogenes , Staphylococcus aureus and Pseudomonas aeruginosa , produce a variety of enzymes which cause damage to host tissues. Enzymes include hyaluronidase , which breaks down the connective tissue component hyaluronic acid ;
10506-478: The viruses express oncogenes that promote cancer cell proliferation. In cancers, these episomes passively replicate together with host chromosomes when the cell divides. When these viral episomes initiate lytic replication to generate multiple virus particles, they generally activate cellular innate immunity defense mechanisms that kill the host cell. Some plasmids or microbial hosts include an addiction system or postsegregational killing system (PSK), such as
10609-472: The years and researchers have given out plasmids to plasmid databases such as the non-profit organisations Addgene and BCCM/GeneCorner . One can find and request plasmids from those databases for research. Researchers also often upload plasmid sequences to the NCBI database , from which sequences of specific plasmids can be retrieved. Extrachromosomal DNA In prokaryotes , nonviral extrachromosomal DNA
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