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Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading
evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
ary theory of the origin of
eukaryotic Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the ...
cells from
prokaryotic A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes (more closely related to the
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
than to the Archaea) taken one inside the other in
endosymbiosis An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
. Mitochondria appear to be phylogenetically related to
Rickettsiales The Rickettsiales, informally called rickettsias, are an order of small Alphaproteobacteria. They are obligate intracellular parasites, and some are notable pathogens, including ''Rickettsia'', which causes a variety of diseases in humans, and ' ...
bacteria, while chloroplasts are thought to be related to cyanobacteria. The idea that chloroplasts were originally independent organisms that merged into a symbiotic relationship with other one-celled organisms dates back to the 19th century, when it was espoused by researchers such as
Andreas Schimper Andreas Franz Wilhelm Schimper (12 May 1856 – 9 September 1901) was a German botanist and phytogeographer who made major contributions in the fields of histology, ecology and plant geography. He travelled to South East Asia and the Caribbea ...
. The endosymbiotic theory was articulated in 1905 and 1910 by the Russian botanist
Konstantin Mereschkowski Konstantin Sergeevich Mereschkowski ( rus, Константи́н Серге́евич Мережко́вский, p=mʲɪrʲɪˈʂkofskʲɪj; – 9 January 1921) was a prominent Russian biologist and botanist, active mainly around Kazan, Tat ...
, and advanced and substantiated with microbiological evidence by
Lynn Margulis Lynn Margulis (born Lynn Petra Alexander; March 5, 1938 – November 22, 2011) was an American evolutionary biologist, and was the primary modern proponent for the significance of symbiosis in evolution. Historian Jan Sapp has said that "Lynn Ma ...
in 1967. Among the many lines of evidence supporting symbiogenesis are that new mitochondria and plastids are formed only by splitting in two, and that cells cannot create new ones otherwise; that the
transport protein A transport protein (variously referred to as a transmembrane pump, transporter, escort protein, acid transport protein, cation transport protein, or anion transport protein) is a protein that serves the function of moving other materials within ...
s called
porins Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse. Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they act as channels tha ...
are found in the outer membranes of mitochondria, chloroplasts, and bacterial cell membranes; that cardiolipin is found only in the inner mitochondrial membrane and bacterial cell membranes; and that some mitochondria and plastids contain single circular DNA molecules similar to the
circular chromosome A circular chromosome is a chromosome in bacteria, archaea, Mitochondrial DNA#Genome structure and diversity, mitochondria, and Chloroplast DNA#Molecular structure, chloroplasts, in the form of a molecule of circular DNA, unlike the linear chromo ...
s of bacteria.


History

The
Russian Russian(s) refers to anything related to Russia, including: *Russians (, ''russkiye''), an ethnic group of the East Slavic peoples, primarily living in Russia and neighboring countries *Rossiyane (), Russian language term for all citizens and peo ...
botanist
Konstantin Mereschkowski Konstantin Sergeevich Mereschkowski ( rus, Константи́н Серге́евич Мережко́вский, p=mʲɪrʲɪˈʂkofskʲɪj; – 9 January 1921) was a prominent Russian biologist and botanist, active mainly around Kazan, Tat ...
first outlined the theory of symbiogenesis (from
Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
: σύν ''syn'' "together", βίος ''bios'' "life", and γένεσις ''genesis'' "origin, birth") in his 1905 work, ''The nature and origins of chromatophores in the plant kingdom'', and then elaborated it in his 1910 ''The Theory of Two Plasms as the Basis of Symbiogenesis, a New Study of the Origins of Organisms''.(journal URL

Mereschkowski knew of the work of botanist Andreas Franz Wilhelm Schimper, Andreas Schimper. In 1883, Schimper had observed that the division of chloroplasts in green plants closely resembled that of free-living cyanobacteria. He had tentatively proposed (in a footnote) that green plants had arisen from a symbiotic union of two organisms. In 1918 the French scientist Paul Jules Portier published ''Les Symbiotes'', in which he claimed that the mitochondria originated from a symbiosis process.
Ivan Wallin Ivan Emanuel Wallin (22 January 1883 – 6 March 1969) was an American biologist who made the first experimental works on endosymbiotic theory. Nicknamed the "Mitochondria Man", he claimed that mitochondria, which are cell organelles, were once i ...
advocated the idea of an endosymbiotic origin of mitochondria in the 1920s. The Russian botanist
Boris Kozo-Polyansky Boris Mikhailovich Kozo-Polyansky (; 20 January 1890 – 21 April 1957) was a Soviet and Russian botanist and evolutionary biologist, best known for his seminal work, ''Symbiogenesis: A New Principle of Evolution'', which was the first work to pla ...
became the first to explain the theory in terms of
Darwinian evolution Darwinism is a theory of biological evolution developed by the English naturalist Charles Darwin (1809–1882) and others, stating that all species of organisms arise and develop through the natural selection of small, inherited variations that ...
. In his 1924 book ''A New Principle of Biology. Essay on the Theory of Symbiogenesis'', he wrote, "The theory of symbiogenesis is a theory of selection relying on the phenomenon of symbiosis." These theories did not gain traction until more detailed electron-microscopic comparisons between cyanobacteria and chloroplasts were made, such as by Hans Ris in 1961 and 1962. These, combined with the discovery that plastids and mitochondria contain their own DNA, led to a resurrection of the idea of symbiogenesis in the 1960s.
Lynn Margulis Lynn Margulis (born Lynn Petra Alexander; March 5, 1938 – November 22, 2011) was an American evolutionary biologist, and was the primary modern proponent for the significance of symbiosis in evolution. Historian Jan Sapp has said that "Lynn Ma ...
advanced and substantiated the theory with microbiological evidence in a 1967 paper, ''On the origin of mitosing cells.'' In her 1981 work ''Symbiosis in Cell Evolution'' she argued that eukaryotic cells originated as communities of interacting entities, including endosymbiotic
spirochaete A spirochaete () or spirochete is a member of the phylum Spirochaetota (), (synonym Spirochaetes) which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled (corkscrew-shaped or s ...
s that developed into eukaryotic flagella and cilia. This last idea has not received much acceptance, because flagella lack DNA and do not show ultrastructural similarities to
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
or to archaea (see also:
Evolution of flagella The evolution of flagella is of great interest to biologists because the three known varieties of flagella – (eukaryotic, bacterial, and archaeal) each represent a sophisticated cellular structure that requires the interaction of many differ ...
and
Prokaryotic cytoskeleton The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but advances in visualization technology and structure determination led t ...
). According to Margulis and Dorion Sagan, "Life did not take over the globe by combat, but by networking" (i.e., by cooperation).
Christian de Duve Christian René Marie Joseph, Viscount de Duve (2 October 1917 – 4 May 2013) was a Nobel Prize-winning Belgian cytologist and biochemist. He made serendipitous discoveries of two cell organelles, peroxisome and lysosome, for which he shared ...
proposed that the peroxisomes may have been the first endosymbionts, allowing cells to withstand growing amounts of free molecular oxygen in the Earth's atmosphere. However, it now appears that peroxisomes may be formed ''de novo'', contradicting the idea that they have a symbiotic origin. (Provides evidence that contradicts an endosymbiotic origin of peroxisomes, and suggests instead that they originate evolutionarily from the endoplasmic reticulum) The fundamental theory of symbiogenesis as the origin of mitochondria and chloroplasts is now widely accepted.


From endosymbionts to organelles

Biologists usually distinguish organelles from
endosymbiont An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
s – whole organisms living inside other organisms – by their reduced
genome size Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms of mass in picograms (trillionths (10−12) of a gram, abbreviated pg) or less frequently in daltons, or as the total ...
s. As an endosymbiont evolves into an organelle, most of its genes are transferred to the host cell
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
. The host cell and organelle therefore need to develop a transport mechanism that enables the return of the
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
products needed by the organelle but now manufactured by the cell.


Free-living ancestors

Alphaproteobacteria Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse and ...
were formerly thought to be the free-living organisms most closely related to mitochondria. Later research indicates that mitochondria are most closely related to
Pelagibacterales The Pelagibacterales are an order in the Alphaproteobacteria composed of free-living marine bacteria that make up roughly one in three cells at the ocean's surface. Overall, members of the ''Pelagibacterales'' are estimated to make up between a q ...
bacteria, in particular, those in the SAR11 clade. Nitrogen-fixing filamentous cyanobacteria are the free-living organisms most closely related to plastids. Both cyanobacteria and alphaproteobacteria maintain a large (>6 Mb) genome encoding thousands of proteins. Plastids and mitochondria exhibit a dramatic reduction in genome size when compared with their bacterial relatives. Chloroplast genomes in photosynthetic organisms are normally 120–200kb encoding 20–200 proteins and mitochondrial genomes in humans are approximately 16kb and encode 37 genes, 13 of which are proteins. Using the example of the freshwater
amoeboid An amoeba (; less commonly spelled ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and retracting pseudopo ...
, however, ''
Paulinella ''Paulinella'' is a genus of at least eleven species including both freshwater and marine amoeboids. Its most famous members are the three photosynthetic species ''P. chromatophora'', ''P. micropora'' and ''P. longichromatophora'', the first tw ...
chromatophora'', which contains
chromatophore Chromatophores are cells that produce color, of which many types are pigment-containing cells, or groups of cells, found in a wide range of animals including amphibians, fish, reptiles, crustaceans and cephalopods. Mammals and birds, in contrast, ...
s found to be evolved from cyanobacteria, Keeling and Archibald argue that this is not the only possible criterion; another is that the host cell has assumed control of the regulation of the former endosymbiont's division, thereby synchronizing it with the cell's own division. Nowack and her colleagues gene sequenced the chromatophore (1.02Mb) and found that only 867 proteins were encoded by these photosynthetic cells. Comparisons with their closest free living cyanobacteria of the genus ''
Synechococcus ''Synechococcus'' (from the Greek ''synechos'', in succession, and the Greek ''kokkos'', granule) is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 to 1.5 µm. The photosynthetic c ...
'' (having a genome size 3Mb, with 3300 genes) revealed that chromatophores had undergone a drastic genome shrinkage. Chromatophores contained genes that were accountable for
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
but were deficient in genes that could carry out other biosynthetic functions; this observation suggests that these endosymbiotic cells are highly dependent on their hosts for their survival and growth mechanisms. Thus, these chromatophores were found to be non-functional for organelle-specific purposes when compared with mitochondria and plastids. This distinction could have promoted the early
evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
of photosynthetic organelles. The loss of genetic autonomy, that is, the loss of many genes from endosymbionts, occurred very early in evolutionary time. Taking into account the entire original endosymbiont genome, there are three main possible fates for genes over evolutionary time. The first is the loss of functionally redundant genes, in which genes that are already represented in the nucleus are eventually lost. The second is the
transfer Transfer may refer to: Arts and media * ''Transfer'' (2010 film), a German science-fiction movie directed by Damir Lukacevic and starring Zana Marjanović * ''Transfer'' (1966 film), a short film * ''Transfer'' (journal), in management studies ...
of genes to the nucleus, while the third is that genes remain in the organelle that was once an organism. The loss of autonomy and integration of the endosymbiont with its host can be primarily attributed to nuclear gene transfer. As organelle genomes have been greatly reduced over evolutionary time,
nuclear gene A nuclear gene is a gene whose physical DNA nucleotide sequence is located in the cell nucleus of a eukaryote. The term is used to distinguish nuclear genes from genes found in mitochondria or chloroplasts. The vast majority of genes in eukary ...
s have expanded and become more complex. As a result, many plastid and mitochondrial processes are driven by nuclear encoded gene products. In addition, many nuclear genes originating from endosymbionts have acquired novel functions unrelated to their organelles.


Gene transfer mechanisms

The mechanisms of gene transfer are not fully known; however, multiple hypotheses exist to explain this phenomenon. The possible mechanisms include the
Complementary DNA In genetics, complementary DNA (cDNA) is DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA (miRNA)) template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to express a spec ...
(cDNA) hypothesis and the bulk flow hypothesis. The cDNA hypothesis involves the use of messenger RNA (mRNAs) to transport genes from organelles to the nucleus where they are converted to cDNA and incorporated into the genome. The cDNA hypothesis is based on studies of the genomes of flowering plants. Protein coding RNAs in mitochondria are spliced and edited using organelle-specific splice and editing sites. Nuclear copies of some mitochondrial genes, however, do not contain organelle-specific splice sites, suggesting a processed mRNA intermediate. The cDNA hypothesis has since been revised as edited mitochondrial cDNAs are unlikely to recombine with the nuclear genome and are more likely to recombine with their native mitochondrial genome. If the edited mitochondrial sequence recombines with the mitochondrial genome, mitochondrial splice sites would no longer exist in the mitochondrial genome. Any subsequent nuclear gene transfer would therefore also lack mitochondrial splice sites. The bulk flow hypothesis is the alternative to the cDNA hypothesis, stating that escaped DNA, rather than mRNA, is the mechanism of gene transfer. According to this hypothesis, disturbances to organelles, including autophagy (normal cell destruction),
gametogenesis Gametogenesis is a biological process by which diploid or haploid precursor cells undergo cell division and differentiation to form mature haploid gametes. Depending on the biological life cycle of the organism, gametogenesis occurs by meiotic di ...
(the formation of gametes), and cell stress release DNA which is imported into the nucleus and incorporated into the nuclear DNA using
non-homologous end joining Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology direc ...
(repair of double stranded breaks). For example, in the initial stages of endosymbiosis, due to a lack of major gene transfer, the host cell had little to no control over the endosymbiont. The endosymbiont underwent cell division independently of the host cell, resulting in many "copies" of the endosymbiont within the host cell. Some of the endosymbionts lysed (burst), and high levels of DNA were incorporated into the nucleus. A similar mechanism is thought to occur in tobacco plants, which show a high rate of gene transfer and whose cells contain multiple chloroplasts. In addition, the bulk flow hypothesis is also supported by the presence of non-random clusters of organelle genes, suggesting the simultaneous movement of multiple genes. Ford Doolittle proposed that (whatever the mechanism) gene transfer behaves like a ratchet, resulting in unidirectional transfer of genes from the organelle to the nuclear genome. When genetic material from an organelle is incorporated into the nuclear genome, either the organelle or nuclear copy of the gene may be lost from the population. If the organelle copy is lost and this is fixed, or lost through genetic drift, a gene is successfully transferred to the nucleus. If the nuclear copy is lost, horizontal gene transfer can occur again, and the cell can ‘try again’ to have successful transfer of genes to the nucleus. In this ratchet-like way, genes from an organelle would be expected to accumulate in the nuclear genome over evolutionary time.


Endosymbiosis of protomitochondria

Endosymbiotic theory for the origin of mitochondria suggests that the proto-eukaryote engulfed a protomitochondrion, and this endosymbiont became an organelle.


Mitochondria

Mitochondria are organelles that synthesize the energy-carrying molecule ATP for the cell by
metabolizing Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...
carbon-based macromolecules. The presence of DNA in mitochondria and proteins, derived from
mtDNA Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial DNA ...
, suggest that this organelle may have been a
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...
prior to its integration into the proto- eukaryote. Mitochondria are regarded as organelles rather than endosymbionts because mitochondria and the host cells share some parts of their
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
, undergo mitosis simultaneously, and provide each other with means to produce energy. The
endomembrane system The endomembrane system is composed of the different membranes (endomembranes) that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments, or organelles. In eukaryotes ...
and
nuclear membrane The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material. The nuclear envelope consists of two lipid bilayer membra ...
were hypothesized to have derived from the protomitochondria.


Nuclear membrane

The presence of a nucleus is one major difference between eukaryotes and
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...
s. Some conserved
nuclear protein A nuclear protein is a protein found in the cell nucleus. Proteins are transported inside the nucleus with the help of the nuclear pore complex, which acts a barrier between cytoplasm and nuclear membrane. The import and export of proteins through ...
s between eukaryotes and prokaryotes suggest that these two types had a common ancestor. Another theory behind nucleation is that early nuclear membrane proteins caused the
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
to fold and form a sphere with pores like the nuclear envelope. As a way of forming a nuclear membrane, endosymbiosis could be expected to use less energy than if the cell was to develop a metabolic process to fold the cell membrane for the purpose. Digesting engulfed cells without energy-producing mitochondria would have been challenging for the host cell. On this view, membrane-bound bubbles or
vesicles Vesicle may refer to: ; In cellular biology or chemistry * Vesicle (biology and chemistry), a supramolecular assembly of lipid molecules, like a cell membrane * Synaptic vesicle ; In human embryology * Vesicle (embryology), bulge-like features o ...
leaving the protomitochondria may have formed the nuclear envelope. The process of symbiogenesis by which the early
eukaryotic cell Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
integrated the proto- mitochondrion likely included protection of the archaeal host
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
from the release of
reactive oxygen species In chemistry, reactive oxygen species (ROS) are highly reactive chemicals formed from diatomic oxygen (). Examples of ROS include peroxides, superoxide, hydroxyl radical, singlet oxygen, and alpha-oxygen. The reduction of molecular oxygen () p ...
. These would have been formed during oxidative phosphorylation and ATP production by the proto-mitochondrion. The
nuclear membrane The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material. The nuclear envelope consists of two lipid bilayer membra ...
may have evolved as an adaptive innovation for protecting against nuclear genome
DNA damage DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA d ...
caused by reactive oxygen species. Substantial transfer of genes from the ancestral proto-mitochondrial genome to the nuclear genome likely occurred during early eukaryotic evolution. The greater protection of the nuclear genome against reactive oxygen species afforded by the nuclear membrane may explain the adaptive benefit of this gene transfer.


Endomembrane system

Modern eukaryotic cells use the endomembrane system to transport products and wastes in, within, and out of cells. The membrane of nuclear envelope and endomembrane vesicles are composed of similar membrane proteins. These vesicles also share similar membrane proteins with the organelle they originated from or are traveling towards. This suggests that what formed the nuclear membrane also formed the endomembrane system. Prokaryotes do not have a complex internal membrane network like eukaryotes, but they could produce extracellular vesicles from their outer membrane. After the early prokaryote was consumed by a proto-eukaryote, the prokaryote would have continued to produce vesicles that accumulated within the cell. Interaction of internal components of vesicles may have led to the endoplasmic reticulum and the
Golgi apparatus The Golgi apparatus (), also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles ...
, both being parts of the endomembrane system.


Organellar genomes


Plastomes and mitogenomes

Some endosymbiont genes remain in the organelles. Plastids and mitochondria retain genes encoding rRNAs, tRNAs, proteins involved in redox reactions, and proteins required for transcription, translation, and replication. There are many hypotheses to explain why organelles retain a small portion of their genome; however no one hypothesis will apply to all organisms, and the topic is still quite controversial. The hydrophobicity hypothesis states that highly
hydrophobic In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, t ...
(water hating) proteins (such as the membrane bound proteins involved in
redox Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or a ...
reactions) are not easily transported through the cytosol and therefore these proteins must be encoded in their respective organelles. The code disparity hypothesis states that the limit on transfer is due to differing genetic codes and RNA editing between the organelle and the nucleus. The redox control hypothesis states that genes encoding redox reaction proteins are retained in order to effectively couple the need for repair and the synthesis of these proteins. For example, if one of the
photosystem Photosystems are functional and structural units of protein complexes involved in photosynthesis. Together they carry out the primary photochemistry of photosynthesis: the absorption of light and the transfer of energy and electrons. Photosystems ...
s is lost from the plastid, the intermediate electron carriers may lose or gain too many electrons, signalling the need for repair of a photosystem. The time delay involved in signalling the nucleus and transporting a cytosolic protein to the organelle results in the production of damaging
reactive oxygen species In chemistry, reactive oxygen species (ROS) are highly reactive chemicals formed from diatomic oxygen (). Examples of ROS include peroxides, superoxide, hydroxyl radical, singlet oxygen, and alpha-oxygen. The reduction of molecular oxygen () p ...
. The final hypothesis states that the assembly of membrane proteins, particularly those involved in redox reactions, requires coordinated synthesis and assembly of subunits; however, translation and protein transport coordination is more difficult to control in the cytoplasm.


Non-photosynthetic plastid genomes

The majority of the genes in the mitochondria and plastids are related to the expression (transcription, translation and replication) of genes encoding proteins involved in either photosynthesis (in plastids) or cellular respiration (in mitochondria). One might predict that the loss of photosynthesis or cellular respiration would allow for the complete loss of the plastid genome or the mitochondrial genome respectively. While there are numerous examples of mitochondrial descendants (
mitosome A mitosome is an organelle found in some unicellular eukaryotic organisms, like in members of the supergroup Excavata. The mitosome was found and named in 1999, and its function has not yet been well characterized. It was termed a ''crypton'' by ...
s and
hydrogenosome A hydrogenosome is a membrane-enclosed organelle found in some anaerobic ciliates, flagellates, and fungi. Hydrogenosomes are highly variable organelles that have presumably evolved from protomitochondria to produce molecular hydrogen and ATP i ...
s) that have lost their entire organellar genome, non-photosynthetic plastids tend to retain a small genome. There are two main hypotheses to explain this occurrence: The essential tRNA hypothesis notes that there have been no documented functional plastid-to-nucleus gene transfers of genes encoding RNA products (tRNAs and rRNAs). As a result, plastids must make their own functional RNAs or import nuclear counterparts. The genes encoding tRNA-Glu and tRNA-fmet, however, appear to be indispensable. The plastid is responsible for
haem Heme, or haem (pronounced /Help:IPA/English, hi:m/ ), is a precursor (chemistry), precursor to hemoglobin, which is necessary to bind oxygen in the bloodstream. Heme is biosynthesized in both the bone marrow and the liver. In biochemical terms, ...
biosynthesis, which requires plastid encoded tRNA-Glu (from the gene trnE) as a precursor molecule. Like other genes encoding RNAs, trnE cannot be transferred to the nucleus. In addition, it is unlikely trnE could be replaced by a
cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells ( intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...
ic tRNA-Glu as trnE is highly conserved; single base changes in trnE have resulted in the loss of haem synthesis. The gene for tRNA-
formylmethionine ''N''-Formylmethionine (fMet, HCO-Met, For-Met) is a derivative of the amino acid methionine in which a formyl group has been added to the amino group. It is specifically used for initiation of protein synthesis from bacterial and organellar g ...
(tRNA-fmet) is also encoded in the plastid genome and is required for translation initiation in both plastids and mitochondria. A plastid is required to continue expressing the gene for tRNA-fmet so long as the mitochondrion is translating proteins. The limited window hypothesis offers a more general explanation for the retention of genes in non-photosynthetic plastids. According to this hypothesis, genes are transferred to the nucleus following the disturbance of organelles. Disturbance was common in the early stages of endosymbiosis, however, once the host cell gained control of organelle division, eukaryotes could evolve to have only one plastid per cell. Having only one plastid severely limits gene transfer as the lysis of the single plastid would likely result in cell death. Consistent with this hypothesis, organisms with multiple plastids show an 80-fold increase in plastid-to-nucleus gene transfer compared with organisms with single plastids.


Evidence

There are many lines of evidence that mitochondria and plastids including chloroplasts arose from bacteria.
Kimball, J. 2010. ''Kimball's Biology Pages''. Accessed October 13, 2010. An online open source biology text by Harvard professor, and author of a general biology text, John W. Kimball.
Reece, J., Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson, 2010. ''Campbell Biology.'' 9th Edition Benjamin Cummings; 9th Ed. (October 7, 2010) * New mitochondria and plastids are formed only through
binary fission Binary may refer to: Science and technology Mathematics * Binary number, a representation of numbers using only two digits (0 and 1) * Binary function, a function that takes two arguments * Binary operation, a mathematical operation that ta ...
, the form of cell division used by bacteria and archaea. * If a cell's mitochondria or chloroplasts are removed, the cell does not have the means to create new ones. In some algae, such as ''
Euglena ''Euglena'' is a genus of single cell flagellate eukaryotes. It is the best known and most widely studied member of the class Euglenoidea, a diverse group containing some 54 genera and at least 200 species. Species of ''Euglena'' are found in f ...
'', the plastids can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell: the plastids do not regenerate. *
Transport proteins A transport protein (variously referred to as a transmembrane pump, transporter, escort protein, acid transport protein, cation transport protein, or anion transport protein) is a protein that serves the function of moving other materials within ...
called
porins Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse. Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they act as channels tha ...
are found in the outer membranes of mitochondria and chloroplasts and are also found in bacterial cell membranes. * A
membrane lipid Membrane lipids are a group of compounds (structurally similar to fats and oils) which form the double-layered surface of all cells (lipid bilayer). The three major classes of membrane lipids are phospholipids, glycolipids, and cholesterol. Lipid ...
cardiolipin is exclusively found in the inner mitochondrial membrane and bacterial cell membranes. * Some mitochondria and some plastids contain single circular DNA molecules that are similar to the DNA of
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
both in size and structure. * Genome comparisons suggest a close relationship between mitochondria and Rickettsial bacteria. * Genome comparisons suggest a close relationship between plastids and cyanobacteria. * Many genes in the genomes of mitochondria and chloroplasts have been lost or transferred to the nucleus of the host cell. Consequently, the chromosomes of many eukaryotes contain genes that originated from the genomes of mitochondria and plastids. * Mitochondria and plastids contain their own ribosomes; these are more similar to those of bacteria (70S) than those of eukaryotes. * Proteins created by mitochondria and chloroplasts use
N-formylmethionine ''N''-Formylmethionine (fMet, HCO-Met, For-Met) is a derivative of the amino acid methionine in which a formyl group has been added to the amino group. It is specifically used for initiation of protein synthesis from bacterial and organellar g ...
as the initiating amino acid, as do proteins created by bacteria but not proteins created by eukaryotic nuclear genes or archaea.


Secondary endosymbiosis

Primary endosymbiosis involves the engulfment of a cell by another free living organism. Secondary endosymbiosis occurs when the product of primary endosymbiosis is itself engulfed and retained by another free living eukaryote. Secondary endosymbiosis has occurred several times and has given rise to extremely diverse groups of algae and other eukaryotes. Some organisms can take opportunistic advantage of a similar process, where they engulf an alga and use the products of its photosynthesis, but once the prey item dies (or is lost) the host returns to a free living state. Obligate secondary endosymbionts become dependent on their organelles and are unable to survive in their absence. A secondary endosymbiosis event involving an ancestral
red alga Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
and a
heterotrophic A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...
eukaryote resulted in the evolution and diversification of several other photosynthetic lineages including
Cryptophyta The cryptophyceae are a class of algae, most of which have plastids. About 220 species are known, and they are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape ...
,
Haptophyta The haptophytes, classified either as the Haptophyta, Haptophytina or Prymnesiophyta (named for '' Prymnesium''), are a clade of algae. The names Haptophyceae or Prymnesiophyceae are sometimes used instead. This ending implies classification at ...
, Stramenopiles (or Heterokontophyta), and Alveolata. A possible secondary endosymbiosis has been observed in process in the heterotrophic protist '' Hatena''. This organism behaves like a predator until it ingests a
green alga The green algae (singular: green alga) are a group consisting of the Prasinodermophyta and its unnamed sister which contains the Chlorophyta and Charophyta/Streptophyta. The land plants (Embryophytes) have emerged deep in the Charophyte alga as ...
, which loses its flagella and cytoskeleton but continues to live as a symbiont. ''Hatena'' meanwhile, now a host, switches to photosynthetic nutrition, gains the ability to move towards light, and loses its feeding apparatus. Despite the diversity of organisms containing plastids, the morphology, biochemistry, genomic organisation, and molecular phylogeny of plastid RNAs and proteins suggest a single origin of all extant plastids – although this theory is still debated. Some species including ''
Pediculus humanus ''Pediculus humanus'' is a species of louse that infects humans. It comprises two subspecies: *''Pediculus humanus humanus'' Linnaeus, 1758 – body louse *''Pediculus humanus capitis'' De Geer, 1767 – head louse The head louse (''Pedicu ...
'' (lice) have multiple chromosomes in the mitochondrion. This and the phylogenetics of the genes encoded within the mitochondrion suggest that mitochondria have multiple ancestors, that these were acquired by endosymbiosis on several occasions rather than just once, and that there have been extensive mergers and rearrangements of genes on the several original mitochondrial chromosomes.


Date

The question of when the transition from prokaryotic to eukaryotic form occurred and when the first crown group eukaryotes appeared on earth is still unresolved. The oldest known body fossils that can be positively assigned to the Eukaryota are acanthomorphic
acritarch Acritarchs are organic microfossils, known from approximately 1800 million years ago to the present. The classification is a catch all term used to refer to any organic microfossils that cannot be assigned to other groups. Their diversity refle ...
s from the 1.631 Gya Deonar Formation of India. These fossils can still be identified as derived post-nuclear eukaryotes with a sophisticated, morphology-generating
cytoskeleton The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is com ...
sustained by mitochondria. This fossil evidence indicates that endosymbiotic acquisition of
alphaproteobacteria Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse and ...
must have occurred before 1.6 Gya. Molecular clocks have also been used to estimate the last eukaryotic common ancestor, however these methods have large inherent uncertainty and give a wide range of dates. Reasonable results include the estimate of c. 1.8 Gya. A 2.3 Gya estimate also seems reasonable, and has the added attraction of coinciding with one of the most pronounced biogeochemical perturbations in Earth history, the early Palaeoproterozoic Great Oxygenation Event. The marked increase in atmospheric oxygen concentrations at that time has been suggested as a contributing cause of eukaryogenesis, inducing the evolution of oxygen-detoxifying mitochondria. Alternatively, the Great Oxidation Event might be a consequence of eukaryogenesis, and its impact on the export and burial of organic carbon.


See also

* '' Angomonas deanei'', a protozoan that harbours an obligate bacterial symbiont * '' Hatena arenicola'', a species that appears to be in the process of acquiring an endosymbiont *
Hydrogen hypothesis The hydrogen hypothesis is a model proposed by William F. Martin and Miklós Müller in 1998 that describes a possible way in which the mitochondrion arose as an endosymbiont within a prokaryotic host in the archaea, giving rise to a symbiotic asso ...
, the theory that mitochondria were acquired by hydrogen-dependent archaea, their endosymbionts being facultatively anaerobic bacteria *
Kleptoplasty Kleptoplasty or kleptoplastidy is a symbiotic phenomenon whereby plastids, notably chloroplasts from algae, are sequestered by host organisms. The word is derived from ''Kleptes'' (κλέπτης) which is Greek for thief. The alga is eaten norma ...
, the sequestering of plastids from ingested algae * ''
Mixotricha paradoxa ''Mixotricha paradoxa'' is a species of protozoan that lives inside the gut of the Australian termite species ''Mastotermes darwiniensis''. It is composed of five different organisms: three bacterial ectosymbionts live on its surface for loco ...
'', which itself is a symbiont, contains numerous endosymbiotic bacteria * ''
Parasite Eve Parasite Eve may refer to: * ''Parasite Eve'' (novel), a 1995 Japanese science fiction horror novel by Hideaki Sena * ''Parasite Eve'' (film), a 1997 Japanese science fiction film based on the novel * ''Parasite Eve'' (video game), a 1998 action ...
'', fiction about endosymbiosis * '' Strigomonas culicis'', another protozoan that harbours an obligate bacterial symbiont * Viral eukaryogenesis, hypothesis that the cell nucleus originated from endosymbiosis


References


Further reading

* (General textbook) * * (Discusses theory of origin of eukaryotic cells by incorporating mitochondria and chloroplasts into anaerobic cells with emphasis on 'phage bacterial and putative viral mitochondrial/chloroplast interactions.) * (Recounts evidence that chloroplast-encoded proteins affect transcription of nuclear genes, as opposed to the more well-documented cases of nuclear-encoded proteins that affect mitochondria or chloroplasts.) * (Discusses theories on how mitochondria and chloroplast genes are transferred into the nucleus, and also what steps a gene needs to go through in order to complete this process.) * *


External links


Tree of Life Eukaryotes
{{DEFAULTSORT:Symbiogenesis Biological hypotheses Endosymbiotic events Evolutionary biology Symbiosis