Symbiogenesis

thumb|upright=2.2|In the theory of symbiogenesis, a merger of an [[archaean and an aerobic bacterium some 2.2 Gya created the eukaryotes, with aerobic mitochondria; a second merger some 1.6 Gya added chloroplasts, creating the green plants. The original theory by Lynn Margulis proposed an additional preliminary merger, but this is poorly supported and not now generally believed.]]

Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms.]]

The Russian botanist Konstantin Mereschkowski first outlined the theory of symbiogenesis (from Greek: 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. Mereschkowski proposed that complex life-forms had originated by two episodes of symbiogenesis, the incorporation of symbiotic bacteria to form successively nuclei and chloroplasts. 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 advocated the idea of an endosymbiotic origin of mitochondria in the 1920s.

The Russian botanist Boris Kozo-Polyansky became the first to explain the theory in terms of Darwinian evolution. 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 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 spirochaetes 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 or to archaea (see also: Evolution of flagella and Prokaryotic cytoskeleton). 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 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. The fundamental theory of symbiogenesis as the origin of mitochondria and chloroplasts is now widely accepted.

Symbiogenesis revolutionized the history of evolution by proposing a mechanism for evolutionary development not encompassed in the original Darwininan vision. Symbiogenesis demonstrated that major evolutionary advancements, particularly the origin of eukaryotic cells, may have resulted from symbiotic mergers rather than from gradual mutations and individual competition, i.e., classical natural selection. Accordingly, symbiogenic theory suggests that endosymbiosis may be a powerful force in generating evolutionary novelty, beyond that which can be explained by natural selection alone.

From endosymbionts to organelles

thumb|upright=2|An [[Eukaryote#Autogenous models|autogenous model of the origin of eukaryotic cells. Evidence now shows that a mitochondrion-less eukaryote has never existed, i.e. the nucleus was acquired at the same time as the mitochondria.]]

Biologists usually distinguish organelles from endosymbionts – whole organisms living inside other organisms – by their reduced genome sizes. As an endosymbiont evolves into an organelle, most of its genes are transferred to the host cell genome. The host cell and organelle therefore need to develop a transport mechanism that enables the return of the protein products needed by the organelle but now manufactured by the cell. More recent research has indicated further that mitochondria are most closely related to the subclade of Alphaproteobacteria known as Pelagibacterales 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 (>6Mb) genome encoding thousands of proteins. encoding 20–200 proteins Using the example of the freshwater amoeboid, however, Paulinella chromatophora, which contains chromatophores 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.

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, The loss of autonomy and integration of the endosymbiont with its host can be primarily attributed to nuclear gene transfer. 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.

Mitochondria

thumb|upright=1.5|[[Endosymbiont|Internal symbiont: mitochondrion has a matrix and membranes, like a free-living alphaproteobacterial cell, from which it may derive.]]

Mitochondria are organelles that synthesize the energy-carrying molecule ATP for the cell by metabolizing carbon-based macromolecules. The presence of DNA in mitochondria and proteins, derived from mtDNA, suggest that this organelle may have been a prokaryote 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, undergo division simultaneously, and provide each other with means to produce energy.

Nuclear membrane

The presence of a nucleus is one major difference between eukaryotes and prokaryotes. Some conserved nuclear proteins 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 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. 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

thumb|upright=1.5|Diagram of endomembrane system in eukaryotic cell

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. In 2020, the same team updated their syntrophy proposal to cover an promethearchaeon that produced hydrogen with deltaproteobacterium that oxidised sulphur. A third organism, an alphaproteobacterium able to respire both aerobically and anaerobically, and to oxidise sulphur, developed into the mitochondrion; it may possibly also have been able to photosynthesise.

Date

The question of when the transition from prokaryotic to eukaryotic form occurred and when the first crown group eukaryotes appeared on earth is unresolved. The oldest known body fossils that can be positively assigned to the Eukaryota are acanthomorphic acritarchs 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 sustained by mitochondria. This fossil evidence indicates that endosymbiotic acquisition of alphaproteobacteria 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.

Organellar genomes

Plastomes and mitogenomes

thumb|upright=1.5|The [[Human mitochondrial genetics|human mitochondrial genome has retained genes encoding 2 rRNAs (blue), 22 tRNAs (white), and 13 redox proteins (yellow, orange, red).]]

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 (water hating) proteins (such as the membrane bound proteins involved in redox 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 photosystems 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. 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. non-photosynthetic plastids tend to retain a small genome. There are two main hypotheses to explain this occurrence: According to this hypothesis, genes are transferred to the nucleus following the disturbance of organelles.

New mitochondria and plastids are formed only through binary fission, 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, 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 called porins are found in the outer membranes of mitochondria and chloroplasts and are also found in bacterial cell membranes.
A membrane 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 both in size and structure.
Genome comparisons suggest a close relationship between mitochondria and Alphaproteobacteria.
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.
Proteins created by mitochondria and chloroplasts use N-formylmethionine 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 and a heterotrophic eukaryote resulted in the evolution and diversification of several other photosynthetic lineages including Cryptophyta, Haptophyta, 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, 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 was still being debated in 2008.

Nitroplasts

A unicellular marine alga, Braarudosphaera bigelowii (a coccolithophore, which is a eukaryote), has been found with a cyanobacterium as an endosymbiont. The cyanobacterium forms a nitrogen-fixing structure, dubbed the nitroplast. It divides evenly when the host cell undergoes mitosis, and many of its proteins derive from the host alga, implying that the endosymbiont has proceeded far along the path towards becoming an organelle. The cyanobacterium is named Candidatus Atelocyanobacterium thalassa, and is abbreviated UCYN-A. The alga is the first eukaryote known to have the ability to fix nitrogen.

References

External links

Tree of Life Eukaryotes