In biology and medicine, a host is an organism that harbours a parasitic, a mutualistic, or a commensalist guest, the guest being provided with nourishment and shelter. Examples include animals playing host to parasitic worms, cells harbouring pathogenic viruses, a bean plant hosting mutualistic nitrogen-fixing bacteria. More in botany, a host plant supplies food resources to micropredators, which have an evolutionarily stable relationship with their hosts similar to ectoparasitism; the host range is the collection of hosts. Symbiosis spans a wide variety of possible relationships between organisms, differing in their permanence and their effects on the two parties. If one of the partners in an association is much larger than the other, it is known as the host. In parasitism, the parasite benefits at the host's expense. In commensalism, the two live together without harming each other, while in mutualism, both parties benefit. Most parasites are only parasitic for part of their life cycle. By comparing parasites with their closest free-living relatives, parasitism has been shown to have evolved on at least 233 separate occasions.
Some organisms live in close association with a host and only become parasitic when environmental conditions deteriorate. A parasite may have a long term relationship with its host; the guest seeks out the host and obtains food or another service from it, but does not kill it. In contrast, a parasitoid spends a large part of its life within or on a single host causing the host's death, with some of the strategies involved verging on predation; the host is kept alive until the parasitoid is grown and ready to pass on to its next life stage. A guest's relationship with its host may be intermittent or temporary associated with multiple hosts, making the relationship equivalent to the herbivory of a wild-living animal. Another possibility is that the host–guest relationship may have no permanent physical contact, as in the brood parasitism of the cuckoo. Parasites follow a wide variety of evolutionary strategies, placing their hosts in an wide range of relationships. Parasitism implies host–parasite coevolution, including the maintenance of gene polymorphisms in the host, where there is a trade-off between the advantage of resistance to a parasite and a cost such as disease caused by the gene.
There are several kinds of host from a parasite's point of view. A definitive or primary host is one. An intermediate host is one. A virus is an obligate parasite, acting as a living thing only to the extent that when it is in a host cell, the machinery of that cell makes copies of the virus. A reservoir host can harbour a pathogen indefinitely with no ill effects, with important implications for disease control. A single reservoir host may be reinfected several times. A host of predilection is the one preferred by a parasite. An amplifying host is one in which the level of pathogen can become high enough that a vector such as a mosquito that feeds on it will become infectious. A secondary or intermediate host harbors a parasite only for a short transition period, during which some developmental stage is completed. For trypanosomes, the cause of sleeping sickness humans are the secondary host, while the tsetse fly is the primary host, given that it has been shown that reproduction occurs in the insect.
Tapeworms and other parasitic flatworms have complex lifecycles, in which specific developmental stages are completed in a sequence of several different hosts. It is not always easy or possible to identify which host is definitive and which secondary; as the life cycles of many parasites are not well understood, sometimes the subjectively more important organism is arbitrarily labelled as definitive, this designation may continue after it is found to be incorrect. For example, sludge worms are sometimes considered "intermediate hosts" for salmonid whirling disease though the myxosporean parasite reproduces sexually inside them. In trichinosis, a disease caused by roundworms, the host has reproductive adults in its digestive tract and immature juveniles in its muscles, is therefore both an intermediate and a definitive host. A paratenic host is similar to an intermediate host, except that it is not needed for the parasite's development cycle to progress. Paratenic hosts serve as "dumps" for non-mature stages of a parasite in which they can accumulate in high numbers.
The trematode Alaria americana may serve as an example: the so-called mesocercarial stages of this parasite reside in tadpoles, which are eaten by the definitive canine host. The tadpoles are more preyed on by snakes, in which the mesocercariae may not undergo further development. However, the parasites may accumulate in the snake paratenic host and infect the definitive host once the snake is consumed by a canid; the nematode Skrjabingylus nasicola is another example, with slugs as the intermediate hosts and rodents as the paratenic hosts, mustelids as the definitive hosts. A dead-end or incidental host is an intermediate host that does not allow transmission to the definitive host, thereby preventing the parasite from completing its development. For example and horses are dead-end hosts for West Nile virus, whose life cycle is between culicine mosquitoes and birds. People and horses can become infected, but the level of virus in their blood does not become high enough to pass on the infection to mosquitoes that bite them.
Micropredation is an evolutionarily stable strategy within parasitism, in w
Archaea constitute a domain of single-celled microorganisms. These microbes are prokaryotes. Archaea were classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the other two domains of life and Eukarya. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in the laboratory and were only detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are similar in size and shape, although a few archaea have shapes quite unlike that of bacteria, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols.
Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or hydrogen gas. Salt-tolerant archaea use sunlight as an energy source, other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by budding; the first observed archaea were extremophiles, living in harsh environments, such as hot springs and salt lakes with no other organisms, but improved detection tools led to the discovery of archaea in every habitat, including soil and marshlands. They are part of the microbiota of all organisms, in the human microbiota they are important in the gut, on the skin. Archaea are numerous in the oceans, the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life, may play roles in the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known. Instead they are mutualists or commensals, such as the methanogens that inhabit the gastrointestinal tract in humans and ruminants, where their vast numbers aid digestion.
Methanogens are used in biogas production and sewage treatment, biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents. For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry and metabolism. For example, microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, the substances they consume. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other; this phylogenetic approach is the main method used today. Archaea – at that time only the methanogens were known – were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox based on their ribosomal RNA genes, they called these groups the Urkingdoms of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms.
Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. Lack of peptidoglycan in their cell walls, 2. Two unusual coenzymes, 3. Results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Otto Kandler and Mark Wheelis proposed reclassifying organisms into three natural domains known as the three-domain system: the Eukarya, the Bacteria and the Archaea, in what is now known as "The Woesian Revolution"; the word archaea comes from the Ancient Greek ἀρχαῖα, meaning "ancient things", as the first representatives of the domain Archaea were methanogens and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity, but as new habitats were studied, more organisms were discovered. Extreme halophilic and hyperthermophilic microbes were included in Archaea. For a long time, archaea were seen as extremophiles that only exist in extreme habitats such as hot springs and salt lakes, but by the end of the 20th century, archaea had been identified in non-extreme environments as well.
Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature. This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction to detect prokaryotes from environmental samples by multiplying their ribosomal genes; this allows the detection and identification of organisms that have not been cultured in the laboratory. The classification of archaea, of prokaryotes in general, is a moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors; these classifications rely on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms. Most of the culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans, discovered in 2003, has been given its own phylum, the Nanoarchaeota.
A new phylum Korarchaeota has been proposed. It contains a sm
A bacteriophage known informally as a phage, is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν, "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, may have simple or elaborate structures, their genomes may encode as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found, it is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. One of the densest natural sources for phages and other viruses is seawater, where up to 9x108 virions per millilitre have been found in microbial mats at the surface, up to 70% of marine bacteria may be infected by phages, they have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe as well as in France.
They are seen as a possible therapy against multi-drug-resistant strains of many bacteria. Phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and shelter the bacteria from drugs meant to eradicate disease, thus promoting persistent infection. Additionally, Inoviridae leave the host cell intact meaning that they can not be used medically anyway. Bacteriophages occur abundantly in the biosphere, with different genomes, lifestyles. Phages are classified by the International Committee on Taxonomy of Viruses according to morphology and nucleic acid. Nineteen families are recognized by the ICTV that infect bacteria and archaea. Of these, only two families have RNA genomes, only five families are surrounded by an envelope. Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA genomes have circular genomes. Nine families infect bacteria only, nine infect archaea only, one infects both bacteria and archaea.
It has been suggested that members of Picobirnaviridae infect bacteria, not mammals. In 1896, Ernest Hanbury Hankin reported that something in the waters of the Ganges and Yamuna rivers in India had marked antibacterial action against cholera and could pass through a fine porcelain filter. In 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria, he believed. Twort's work was interrupted by shortage of funding. Independently, French-Canadian microbiologist Félix d'Hérelle, working at the Pasteur Institute in Paris, announced on 3 September 1917, that he had discovered "an invisible, antagonistic microbe of the dysentery bacillus". For d’Hérelle, there was no question as to the nature of his discovery: "In a flash I had understood: what caused my clear spots was in fact an invisible microbe … a virus parasitic on bacteria." D'Hérelle called the virus a bacteria-eater. He recorded a dramatic account of a man suffering from dysentery, restored to good health by the bacteriophages.
It was D'Herelle who conducted much research into bacteriophages and introduced the concept of phage therapy. In 1969, Max Delbrück, Alfred Hershey and Salvador Luria were awarded the Nobel Prize in Physiology or Medicine for their discoveries of the replication of viruses and their genetic structure. Phages were discovered to be antibacterial agents and were used in the former Soviet Republic of Georgia during the 1920s and 1930s for treating bacterial infections, they had widespread use, including treatment of soldiers in the Red Army. However, they were abandoned for general use in the West for several reasons: Antibiotics were discovered and marketed widely, they were easier to store and to prescribe. Medical trials of phages were carried out, but a basic lack of understanding raised questions about the validity of these trials. Publication of research in the Soviet Union was in the Russian or Georgian languages and were not followed internationally for many years; the use of phages has continued since the end of the Cold War in Georgia and elsewhere in Central and Eastern Europe.
The first regulated, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous ulcers of the leg in human patients. The FDA approved the study as a Phase I clinical trial; the study's results demonstrated the safety of therapeutic application of bacteriophages but did not show efficacy. The authors explain that the use of certain chemicals that are part of standard wound care may have interfered with bacteriophage viability. Another controlled clinical trial in Western Europe was reported shortly after this in the journal Clinical Otolaryngology in August 2009; the study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for
International Code of Nomenclature for algae, fungi, and plants
The International Code of Nomenclature for algae and plants is the set of rules and recommendations dealing with the formal botanical names that are given to plants, fungi and a few other groups of organisms, all those "traditionally treated as algae, fungi, or plants". It was called the International Code of Botanical Nomenclature; the current version of the code is the Shenzhen Code adopted by the International Botanical Congress held in Shenzhen, China, in July 2017. As with previous codes, it took effect as soon as it was ratified by the congress, but the documentation of the code in its final form was not published until 26 June 2018; the name of the Code is capitalized and not. The lower-case for "algae and plants" indicates that these terms are not formal names of clades, but indicate groups of organisms that were known by these names and traditionally studied by phycologists and botanists; this includes blue-green algae. There are special provisions in the ICN for some of these groups.
The ICN can only be changed by an International Botanical Congress, with the International Association for Plant Taxonomy providing the supporting infrastructure. Each new edition supersedes the earlier editions and is retroactive back to 1753, except where different starting dates are specified. For the naming of cultivated plants there is a separate code, the International Code of Nomenclature for Cultivated Plants, which gives rules and recommendations that supplement the ICN. Botanical nomenclature is independent of zoological and viral nomenclature. A botanical name is fixed to a taxon by a type; this is invariably dried plant material and is deposited and preserved in a herbarium, although it may be an image or a preserved culture. Some type collections can be viewed online at the websites of the herbaria in question. A guiding principle in botanical nomenclature is priority, the first publication of a name for a taxon; the formal starting date for purposes of priority is 1 May 1753, the publication of Species Plantarum by Linnaeus.
However, to avoid undesirable effects of strict enforcement of priority, conservation of family and species names is possible. The intent of the Code is that each taxonomic group of plants has only one correct name, accepted worldwide, provided that it has the same circumscription and rank; the value of a scientific name is. Names of taxa are treated as Latin; the rules of nomenclature are retroactive unless there is an explicit statement that this does not apply. The rules governing botanical nomenclature have a long and tumultuous history, dating back to dissatisfaction with rules that were established in 1843 to govern zoological nomenclature; the first set of international rules was the Lois de la nomenclature botanique, adopted as the "best guide to follow for botanical nomenclature" at an "International Botanical Congress" convened in Paris in 1867. Unlike modern codes, it was not enforced, it was organized as six sections with 68 articles in total. Multiple attempts to bring more "expedient" or more equitable practice to botanical nomenclature resulted in several competing codes, which reached a compromise with the 1930 congress.
In the meantime, the second edition of the international rules followed the Vienna congress in 1905. These rules were published as the Règles internationales de la Nomenclature botanique adoptées par le Congrès International de Botanique de Vienne 1905. Informally they are referred to as the Vienna Rules; some but not all subsequent meetings of the International Botanical Congress have produced revised versions of these Rules called the International Code of Botanical Nomenclature, International Code of Nomenclature for algae and plants. The Nomenclature Section of the 18th International Botanical Congress in Melbourne, Australia made major changes: The Code now permits electronic-only publication of names of new taxa; the requirement for a Latin validating diagnosis or description was changed to allow either English or Latin for these essential components of the publication of a new name. "One fungus, one name" and "one fossil, one name" are important changes. As an experiment with "registration of names", new fungal descriptions require the use of an identifier from "a recognized repository".
Some important versions are listed below. Specific to botany Author citation Botanical name Botanical nomenclature International Association for Plant Taxonomy International Code of Nomenclature for Cultivated Plants International Plant Names Index Correct name Infraspecific name Hybrid name More general Glossary of scientific naming Binomial nomenclature Nomenclature codes Scientific classification Undescribed species
Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. RNA polymerase transcribes primary transcript mRNA into processed, mature mRNA; this mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology. As in DNA, mRNA genetic information is in the sequence of nucleotides, which are arranged into codons consisting of three base pairs each; each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. This process of translation of codons into amino acids requires two other types of RNA: Transfer RNA, that mediates recognition of the codon and provides the corresponding amino acid, ribosomal RNA, the central component of the ribosome's protein-manufacturing machinery; the existence of mRNA was first suggested by Jacques Monod and François Jacob, subsequently discovered by Jacob, Sydney Brenner and Matthew Meselson at the California Institute of Technology in 1961.
It should not be confused with mitochondrial DNA. The brief existence of an mRNA molecule begins with transcription, ends in degradation. During its life, an mRNA molecule may be processed and transported prior to translation. Eukaryotic mRNA molecules require extensive processing and transport, while prokaryotic mRNA molecules do not. A molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when RNA is made from DNA. During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed; this process is similar in prokaryotes. One notable difference, however, is that eukaryotic RNA polymerase associates with mRNA-processing enzymes during transcription so that processing can proceed after the start of transcription; the short-lived, unprocessed or processed product is termed precursor mRNA, or pre-mRNA. Processing of mRNA differs among eukaryotes and archea. Non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases.
Eukaryotic pre-mRNA, requires extensive processing. A 5' cap is a modified guanine nucleotide, added to the "front" or 5' end of a eukaryotic messenger RNA shortly after the start of transcription; the 5' cap consists of a terminal 7-methylguanosine residue, linked through a 5'-5'-triphosphate bond to the first transcribed nucleotide. Its presence is critical for recognition by the protection from RNases. Cap addition is coupled to transcription, occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase; this enzymatic complex catalyzes the chemical reactions. Synthesis proceeds as a multi-step biochemical reaction. In some instances, an mRNA will be edited, changing the nucleotide composition of that mRNA. An example in humans is the apolipoprotein B mRNA, edited in some tissues, but not others; the editing creates an early stop codon, upon translation, produces a shorter protein.
Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA molecules are polyadenylated at the 3' end, but recent studies have shown that short stretches of uridine are common; the poly tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is important for transcription termination, export of the mRNA from the nucleus, translation. MRNA can be polyadenylated in prokaryotic organisms, where poly tails act to facilitate, rather than impede, exonucleolytic degradation. Polyadenylation occurs during and/or after transcription of DNA into RNA. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. After the mRNA has been cleaved, around 250 adenosine residues are added to the free 3' end at the cleavage site; this reaction is catalyzed by polyadenylate polymerase. Just as in alternative splicing, there can be more than one polyadenylation variant of an mRNA.
Polyadenylation site mutations occur. The primary RNA transcript of a gene is cleaved at the poly-A addition site, 100–200 A's are added to the 3’ end of the RNA. If this site is altered, an abnormally long and unstable mRNA construct will be formed. Another difference between eukaryotes and prokaryotes is mRNA transport; because eukaryotic transcription and translation is compartmentally separated, eukaryotic mRNAs must be exported from the nucleus to the cytoplasm—a process that may be regulated by different signaling pathways. Mature mRNAs are recognized by their processed modifications and exported through the nuclear pore by binding to the cap-binding proteins CBP20 and CBP80, as well as the transcription/export complex. Multiple mRNA export pathways have been identified in eukaryotes. In spatially complex cells, some mRNAs are transported to particular subcellar destinations. In mature neurons, certain mRNA are transported from the soma to dendrites. One site of mRNA translation is at polyribosomes selectively localized beneath synapses.
The mRNA for Arc/Arg3.1 is induced by synaptic activity and localizes selectively near active synapses based on signals generated by NMDA receptor
Insects or Insecta are hexapod invertebrates and the largest group within the arthropod phylum. Definitions and circumscriptions vary; as used here, the term Insecta is synonymous with Ectognatha. Insects have a chitinous exoskeleton, a three-part body, three pairs of jointed legs, compound eyes and one pair of antennae. Insects are the most diverse group of animals; the total number of extant species is estimated at between ten million. Insects may be found in nearly all environments, although only a small number of species reside in the oceans, which are dominated by another arthropod group, crustaceans. Nearly all insects hatch from eggs. Insect growth is constrained by the inelastic exoskeleton and development involves a series of molts; the immature stages differ from the adults in structure and habitat, can include a passive pupal stage in those groups that undergo four-stage metamorphosis. Insects that undergo three-stage metamorphosis lack a pupal stage and adults develop through a series of nymphal stages.
The higher level relationship of the insects is unclear. Fossilized insects of enormous size have been found from the Paleozoic Era, including giant dragonflies with wingspans of 55 to 70 cm; the most diverse insect groups appear to have coevolved with flowering plants. Adult insects move about by walking, flying, or sometimes swimming; as it allows for rapid yet stable movement, many insects adopt a tripedal gait in which they walk with their legs touching the ground in alternating triangles, composed of the front & rear on one side with the middle on the other side. Insects are the only invertebrates to have evolved flight, all flying insects derive from one common ancestor. Many insects spend at least part of their lives under water, with larval adaptations that include gills, some adult insects are aquatic and have adaptations for swimming; some species, such as water striders, are capable of walking on the surface of water. Insects are solitary, but some, such as certain bees and termites, are social and live in large, well-organized colonies.
Some insects, such as earwigs, show maternal care, guarding their eggs and young. Insects can communicate with each other in a variety of ways. Male moths can sense the pheromones of female moths over great distances. Other species communicate with sounds: crickets stridulate, or rub their wings together, to attract a mate and repel other males. Lampyrid beetles communicate with light. Humans regard certain insects as pests, attempt to control them using insecticides, a host of other techniques; some insects damage crops by feeding on sap, fruits, or wood. Some species are parasitic, may vector diseases; some insects perform complex ecological roles. Insect pollinators are essential to the life cycle of many flowering plant species on which most organisms, including humans, are at least dependent. Many insects are considered ecologically beneficial as predators and a few provide direct economic benefit. Silkworms produce silk and honey bees produce honey and both have been domesticated by humans.
Insects are consumed as food in 80% of the world's nations, by people in 3000 ethnic groups. Human activities have effects on insect biodiversity; the word "insect" comes from the Latin word insectum, meaning "with a notched or divided body", or "cut into", from the neuter singular perfect passive participle of insectare, "to cut into, to cut up", from in- "into" and secare "to cut". A calque of Greek ἔντομον, "cut into sections", Pliny the Elder introduced the Latin designation as a loan-translation of the Greek word ἔντομος or "insect", Aristotle's term for this class of life in reference to their "notched" bodies. "Insect" first appears documented in English in 1601 in Holland's translation of Pliny. Translations of Aristotle's term form the usual word for "insect" in Welsh, Serbo-Croatian, etc; the precise definition of the taxon Insecta and the equivalent English name "insect" varies. In the broadest circumscription, Insecta sensu lato consists of all hexapods. Traditionally, insects defined in this way were divided into "Apterygota" —the wingless insects—and Pterygota—the winged insects.
However, modern phylogenetic studies have shown that "Apterygota" is not monophyletic, so does not form a good taxon. A narrower circumscription restricts insects to those hexapods with external mouthparts, comprises only the last three groups in the table. In this sense, Insecta sensu stricto is equivalent to Ectognatha. In the narrowest circumscription, insects are restricted to hexapods that are either winged or descended from winged ancestors. Insecta sensu strictissimo is equivalent to Pterygota. For the purposes of this article, the middle definition is used; the evolutionary relationship of insects to other animal groups remains unclear. Although traditionally grouped with millipedes and centiped
Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. These DNA sequences use a "copy-and-paste" mechanism, whereby they are first transcribed into RNA converted back into identical DNA sequences using reverse transcription, these sequences are inserted into the genome at target sites. Retrotransposons form one of the two subclasses of transposons, where the others are DNA transposons, which does not involve an RNA intermediate. Retrotransposons are abundant in plants, where they are a principal component of nuclear DNA. In maize, 49–78% of the genome is made up of retrotransposons. In wheat, about 90 % of the genome consists of 68 % of transposable elements. In mammals half the genome is transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons, while DNA transposons account for about 2–3%; the retrotransposons' replicative mode of transposition by means of an RNA intermediate increases the copy numbers of elements and thereby can increase genome size.
Like DNA transposable elements, retrotransposons can induce mutations by inserting near or within genes. Furthermore, retrotransposon-induced mutations are stable, because the sequence at the insertion site is retained as they transpose via the replication mechanism. Retrotransposons copy themselves to RNA and back to DNA that may integrate back to the genome; the second step of forming DNA may be carried out by a reverse transcriptase, which the retrotransposon encodes. Transposition and survival of retrotransposons within the host genome are regulated both by retrotransposon- and host-encoded factors, to avoid deleterious effects on host and retrotransposon as well; the understanding of how retrotransposons and their hosts' genomes have co-evolved mechanisms to regulate transposition, insertion specificities, mutational outcomes in order to optimize each other's survival is still in its infancy. Because of accumulated mutations, most retrotransposons are no longer able to retrotranspose. Retrotransposons known as class I transposable elements, consist of two subclasses, the long terminal repeat and the non-LTR retrotransposons.
Classification into these subclasses is based on the phylogeny of the reverse transcriptase, which goes in line with structural differences, such as presence/absence of long terminal repeats as well as number and types of open reading frames, encoding domains and target site duplication lengths. LTR retrotransposons have direct LTRs. LTR retrotransposons are further sub-classified into the Ty1-copia-like, Ty3-gypsy-like, BEL-Pao-like groups based on both their degree of sequence similarity and the order of encoded gene products. Ty1-copia and Ty3-gypsy groups of retrotransposons are found in high copy number in animals, fungi and plants genomes. BEL-Pao like elements have so far only been found in animals. Although retroviruses are classified separately, they share many features with LTR retrotransposons. A major difference with Ty1-copia and Ty3-gypsy retrotransposons is that retroviruses have an envelope protein. A retrovirus can be transformed into an LTR retrotransposon through inactivation or deletion of the domains that enable extracellular mobility.
If such a retrovirus infects and subsequently inserts itself in the genome in germ line cells, it may become transmitted vertically and become an Endogenous Retrovirus. Endogenous retroviruses make up about 8% of the human genome and 10% of the mouse genome. In plant genomes, LTR retrotransposons are the major repetitive sequence class, e.g. able to constitute more than 75% of the maize genome. Endogenous retroviruses are an important type of LTR retrotransposon in mammals, including in humans where the Human ERVs make up 8% of the genome. Non-LTR retrotransposons consist of two sub-types, long interspersed elements and short interspersed elements, they can be found in high copy numbers, as shown in the plant species. Non-long terminal repeat retroposons are widespread in eukaryotic genomes. LINEs possess two ORFs; these functions include reverse transcriptase and endonuclease activities, in addition to a nucleic acid-binding property needed to form a ribonucleoprotein particle. SINEs, on the other hand, co-opt the LINE function as nonautonomous retroelements.
While viewed as "junk DNA", recent research suggests that, in some rare cases, both LINEs and SINEs were incorporated into novel genes so as to evolve new functionality. Long INterspersed Elements are a group of genetic elements that are found in large numbers in eukaryotic genomes, comprising 17% of the human genome. Among the LINE, there are several subgroups, such as L1, L2 and L3. Human coding L1 begin with an untranslated region that includes an RNA polymerase II promoter, two non-overlapping open reading frames, ends with another UTR. A new open reading frame in the 5' end of the LINE elements has been identified in the reverse strand, it is shown to be transcribed and endogenous proteins are observed. The name ORF0 is coined due to its position with respect to ORF1 and ORF2. ORF1 encodes an RNA binding protein and ORF2 encodes a protein having an endonuclease as well as a reverse transcriptase; the reve