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Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within a methanogenic archaeon or a bacterium. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome and eventually usurping its role. The hypothesis was first proposed by Philip Bell in 2001 [1] and was further popularized with the discovery of large, complex DNA viruses (such as Mimivirus ) that are capable of protein biosynthesis.
Viral eukaryogenesis has been controversial for several reasons. For one, it is sometimes argued that the posited evidence for the viral origins of the nucleus can be conversely used to suggest the nuclear origins of some viruses. [2] Secondly, this hypothesis has further inflamed the longstanding debate over whether viruses are living organisms. [2]
The viral eukaryogenesis hypothesis posits that eukaryotes are composed of three ancestral elements: a viral component that became the modern nucleus; a prokaryotic cell (an archaeon according to the eocyte hypothesis) which donated the cytoplasm and cell membrane of modern cells; and another prokaryotic cell (here bacterium) that, by endocytosis, became the modern mitochondrion or chloroplast.
In 2006, researchers suggested that the transition from RNA to DNA genomes first occurred in the viral world. [3] A DNA-based virus may have provided storage for an ancient host that had previously used RNA to store its genetic information (such host is called ribocell or ribocyte). [2] Viruses may initially have adopted DNA as a way to resist RNA-degrading enzymes in the host cells. Hence, the contribution from such a new component may have been as significant as the contribution from chloroplasts or mitochondria. Following this hypothesis, archaea, bacteria, and eukaryotes each obtained their DNA informational system from a different virus. [3] In the original paper it was also an RNA cell at the origin of eukaryotes, but eventually more complex, featuring RNA processing. Although this is in contrast to nowadays's more probable eocyte hypothesis, viruses seem to have contributed to the origin of all three domains of life ('out of virus hypothesis'). It has also been suggested that telomerase and telomeres, key aspects of eukaryotic cell replication, have viral origins. Further, the viral origins of the modern eukaryotic nucleus may have relied on multiple infections of archaeal cells carrying bacterial mitochondrial precursors with lysogenic viruses. [4]
The viral eukaryogenesis hypothesis depicts a model of eukaryotic evolution in which a virus, similar to a modern pox virus, evolved into a nucleus via gene acquisition from existing bacterial and archaeal species. [5] The lysogenic virus then became the information storage center for the cell, while the cell retained its capacities for gene translation and general function despite the viral genome's entry. Similarly, the bacterial species involved in this eukaryogenesis retained its capacity to produce energy in the form of ATP while also passing much of its genetic information into this new virus-nucleus organelle. It is hypothesized that the modern cell cycle, whereby mitosis, meiosis, and sex occur in all eukaryotes, evolved because of the balances struck by viruses, which characteristically follow a pattern of tradeoff between infecting as many hosts as possible and killing an individual host through viral proliferation. Hypothetically, viral replication cycles may mirror those of plasmids and viral lysogens. However, this theory is controversial, and additional experimentation involving archaeal viruses is necessary, as they are probably the most evolutionarily similar to modern eukaryotic nuclei. [6] [7]
The viral eukaryogenesis hypothesis points to the cell cycle of eukaryotes, particularly sex and meiosis, as evidence. [6] Little is known about the origins of DNA or reproduction in prokaryotic or eukaryotic cells. It is thus possible that viruses were involved in the creation of Earth's first cells. [8] The eukaryotic nucleus contains linear DNA with specialized end sequences, like that of viruses (and in contrast to bacterial genomes, which have a circular topology); it uses mRNA capping, and separates transcription from translation. Eukaryotic nuclei are also capable of cytoplasmic replication. Some large viruses have their own DNA-directed RNA polymerase. [2] Transfers of "infectious" nuclei have been documented in many parasitic red algae. [9]
Recent supporting evidence includes the discovery that upon the infection of a bacterial cell, the giant bacteriophage 201 Φ2-1 (of the genus Phikzvirus ) assembles a nucleus-like structure around the region of genome replication and uncouples transcription and translation, and synthesized mRNA is then transported into the cytoplasm where it undergoes translation. [10] The same researchers also found that this same phage encodes a eukaryotic homologue to tubulin (PhuZ) that plays the role of positioning the viral factory in the center of the cell during genome replication. [11] The PhuZ spindle shares several unique properties with eukaryotic spindles: dynamic instability, bipolar filament arrays, and centrally positioning DNA. [7] Further, many classes of nucleocytoplasmic large DNA viruses (NCLDVs) such as mimiviruses have the apparatus to produce m7G capped mRNA and contain homologues of the eukaryotic cap-binding protein eIF4E. Those supporting viral eukaryogenesis also point to the lack of these features in archaea, and so believe that a sizable gap separates the archaeal groups most related to the eukaryotes and the eukaryotes themselves in terms of the nucleus. In light of these and other discoveries, Bell modified his original thesis to suggest that the viral ancestor of the nucleus was an NCLDV-like archaeal virus rather than a pox-like virus. [7] Another piece of supporting evidence is that the m7G capping apparatus (involved in uncoupling of transcription from translation) is present in both Eukarya and Mimiviridae but not in Lokiarchaeota that are considered the nearest archaeal relatives of Eukarya according to the Eocyte hypothesis (also supported by the phylogenetic analysis of the m7G capping pathway). [7]
Several precepts in the theory are possible. For instance, a helical virus with a bilipid envelope bears a distinct resemblance to a highly simplified cellular nucleus (i.e., a DNA chromosome encapsulated within a lipid membrane). In theory, a large DNA virus could take control of a bacterial or archaeal cell. Instead of replicating and destroying the host cell, it would remain within the cell, thus overcoming the tradeoff dilemma typically faced by viruses. With the virus in control of the host cell's molecular machinery, it would effectively become a functional nucleus. Through the processes of mitosis and cytokinesis, the virus would thus recruit the entire cell as a symbiont—a new way to survive and proliferate. [12]
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A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.
A provirus is a virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages), proviruses are often referred to as prophages. However, proviruses are distinctly different from prophages and these terms should not be used interchangeably. Unlike prophages, proviruses do not excise themselves from the host genome when the host cell is stressed.
Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.
DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
Viral evolution is a subfield of evolutionary biology and virology that is specifically concerned with the evolution of viruses. Viruses have short generation times, and many—in particular RNA viruses—have relatively high mutation rates. Although most viral mutations confer no benefit and often even prove deleterious to viruses, the rapid rate of viral mutation combined with natural selection allows viruses to quickly adapt to changes in their host environment. In addition, because viruses typically produce many copies in an infected host, mutated genes can be passed on to many offspring quickly. Although the chance of mutations and evolution can change depending on the type of virus, viruses overall have high chances for mutations.
Sexual reproduction is an adaptive feature which is common to almost all multicellular organisms and various unicellular organisms. Currently, the adaptive advantage of sexual reproduction is widely regarded as a major unsolved problem in biology. As discussed below, one prominent theory is that sex evolved as an efficient mechanism for producing variation, and this had the advantage of enabling organisms to adapt to changing environments. Another prominent theory, also discussed below, is that a primary advantage of outcrossing sex is the masking of the expression of deleterious mutations. Additional theories concerning the adaptive advantage of sex are also discussed below. Sex does, however, come with a cost. In reproducing asexually, no time nor energy needs to be expended in choosing a mate and, if the environment has not changed, then there may be little reason for variation, as the organism may already be well-adapted. However, very few environments have not changed over the millions of years that reproduction has existed. Hence it is easy to imagine that being able to adapt to changing environment imparts a benefit. Sex also halves the amount of offspring a given population is able to produce. Sex, however, has evolved as the most prolific means of species branching into the tree of life. Diversification into the phylogenetic tree happens much more rapidly via sexual reproduction than it does by way of asexual reproduction.
Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria, and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.
A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό 'before' and κάρυον 'nut, kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota.
Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
Evolution of cells refers to the evolutionary origin and subsequent evolutionary development of cells. Cells first emerged at least 3.8 billion years ago approximately 750 million years after Earth was formed.
The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes. After his team at the University of California, Los Angeles discovered eocytes in 1984, James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: prokaryotes, which include Bacteria and Archaea, and karyotes, that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria.
Spiraviridae is a family of incertae sedis viruses that replicate in hyperthermophilic archaea of the genus Aeropyrum, specifically Aeropyrum pernix. The family contains one genus, Alphaspiravirus, which contains one species, Aeropyrum coil-shaped virus. The virions of ACV are non-enveloped and in the shape of hollow cylinders that are formed by a coiling fiber that consists of two intertwining halves of the circular DNA strand inside a capsid. An appendage protrudes from each end of the cylindrical virion. The viral genome is ssDNA(+) and encodes for significantly more genes than other known ssDNA viruses. ACV is also unique in that it appears to lack its own enzymes to aid replication, instead likely using the host cell's replisomes. ACV has no known relation to any other archaea-infecting viruses, but it does share its coil-like morphology with some other archaeal viruses, suggesting that such viruses may be an ancient lineage that only infect archaea.
TACK is a group of archaea, its name an acronym for Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota, the first groups discovered. They are found in different environments ranging from acidophilic thermophiles to mesophiles and psychrophiles and with different types of metabolism, predominantly anaerobic and chemosynthetic. TACK is a clade that is sister to the Asgard branch that gave rise to the eukaryotes. It has been proposed that the TACK clade be classified as Crenarchaeota and that the traditional "Crenarchaeota" (Thermoproteota) be classified as a class called "Sulfolobia", along with the other phyla with class rank or order.
Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.
In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:
Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.
Varidnaviria is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain a vertical jelly roll fold. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid (DNA), and are perpendicular, or vertical, to the surface of the capsid. Apart from this, viruses in the realm also share many other characteristics, such as minor capsid proteins (mCP) with the vertical jelly roll fold, an ATPase that packages viral DNA into the capsid, and a DNA polymerase that replicates the viral genome.
An archaeal virus is a virus that infects and replicates in archaea, a domain of unicellular, prokaryotic organisms. Archaeal viruses, like their hosts, are found worldwide, including in extreme environments inhospitable to most life such as acidic hot springs, highly saline bodies of water, and at the bottom of the ocean. They have been also found in the human body. The first known archaeal virus was described in 1974 and since then, a large diversity of archaeal viruses have been discovered, many possessing unique characteristics not found in other viruses. Little is known about their biological processes, such as how they replicate, but they are believed to have many independent origins, some of which likely predate the last archaeal common ancestor (LACA).
The two-domain system is a biological classification by which all organisms in the tree of life are classified into two big domains, Bacteria and Archaea. It emerged from development of knowledge of archaea diversity and challenges to the widely accepted three-domain system that defines life into Bacteria, Archaea, and Eukarya. It was preceded by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system, due to evidence at the time. Better understanding of archaea, especially of their roles in the origin of eukaryotes through symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became more widely accepted after the discovery of a large group (superphylum) of archaea called Asgard in 2017, which evidence suggests to be the evolutionary root of eukaryotes, implying that eukaryotes are members of the domain Archaea.
The first universal common ancestor (FUCA) is a proposed non-cellular entity that is the earliest ancestor of the last universal common ancestor (LUCA) and its descendants, including every modern cell. FUCA would also be the ancestor of ancient sister lineages of LUCA, none of which have modern descendants.