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.
In prokaryotes, nonviral extrachromosomal DNA 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 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 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 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.
Prokaryotic
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 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 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 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 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 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 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 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 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.
Eukaryotic
Mitochondrial
Mitochondria present in eukaryotic cells contain multiple copies of mitochondrial DNA (mtDNA) in the mitochondrial matrix. 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 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 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 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 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 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.
+ Coding differences found in the mtDNA sequences of various organisms Genetic code Translation table DNA codon involved RNA codon involved Translation with this code Comparison with the universal code Vertebrate mitochondrial 2AGAAGA Ter (*) Arg (R)AGGAGG Ter (*) Arg (R)ATAAUA Met (M) Ile (I)TGAUGA Trp (W) Ter (*) Yeast mitochondrial 3ATAAUA Met (M) Ile (I)CTTCUU Thr (T) Leu (L)CTCCUC Thr (T) Leu (L)CTACUA Thr (T) Leu (L)CTGCUG Thr (T) Leu (L)TGAUGA Trp (W) Ter (*)CGACGAabsent Arg (R)CGCCGCabsent Arg (R) Mold, protozoan, and coelenterate mitochondrial 4 and 7TGAUGA Trp (W) Ter (*) Invertebrate mitochondrial 5AGAAGA Ser (S) Arg (R)AGGAGG Ser (S) Arg (R)ATAAUA Met (M) Ile (I)TGAUGA Trp (W) Ter (*) Echinoderm and flatworm mitochondrial 9AAAAAA Asn (N) Lys (K)AGAAGA Ser (S) Arg (R)AGGAGG Ser (S) Arg (R)TGAUGA Trp (W) Ter (*) Ascidian mitochondrial 13AGAAGA Gly (G) Arg (R)AGGAGG Gly (G) Arg (R)ATAAUA Met (M) Ile (I)TGAUGA Trp (W) Ter (*) Alternative flatworm mitochondrial 14AAAAAA Asn (N) Lys (K)AGAAGA Ser (S) Arg (R)AGGAGG Ser (S) Arg (R)TAAUAA Tyr (Y) Ter (*)TGAUGA Trp (W) Ter (*) Chlorophycean mitochondrial 16TAGUAG Leu (L) Ter (*) Trematode mitochondrial 21TGAUGA Trp (W) Ter (*)ATAAUA Met (M) Ile (I)AGAAGA Ser (S) Arg (R)AGGAGG Ser (S) Arg (R)AAAAAA Asn (N) Lys (K) Scenedesmus obliquus mitochondrial 22TCAUCA Ter (*) Ser (S)TAGUAG Leu (L) Ter (*) Thraustochytrium mitochondrial 23TTAUUA Ter (*) Leu (L) Pterobranchia mitochondrial 24AGAAGA Ser (S) Arg (R)AGGAGG Lys (K) Arg (R)TGAUGA Trp (W) Ter (*) Amino acids biochemical properties nonpolar polar basic acidic Termination: stop codon
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.
Chloroplast Eukaryotic chloroplasts, as well as the other plant plastids, also contain extrachromosomal DNA molecules. Most chloroplasts house all of their genetic material in a single ringed chromosome, however in some species there is evidence of multiple smaller ringed plasmids. 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 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 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.
Circular