Editing Symbiogenesis (section)

== Endosymbiosis of protomitochondria ==

{{further|Eukaryogenesis}}

Endosymbiotic theory for the origin of mitochondria suggests that the proto-eukaryote engulfed a protomitochondrion, and this endosymbiont became an organelle, a major step in [[eukaryogenesis]], the creation of the eukaryotes.<ref name=":12">{{cite journal |last1=Zimorski |first1=Verena |last2=Ku |first2=Chuan |last3=Martin |first3=William F |last4=Gould |first4=Sven B |title=Endosymbiotic theory for organelle origins |journal=[[Current Opinion in Microbiology]] |volume=22 |year=2014 |doi=10.1016/j.mib.2014.09.008 |pages=38–48|pmid=25306530 }}</ref>

=== Mitochondria ===

[[File:Mitochondria, mammalian lung - TEM.jpg|thumb|upright=1.5|[[Endosymbiont|Internal symbiont]]: [[mitochondrion]] has a [[Matrix (biology)|matrix]] and membranes, like a free-living [[alphaproteobacteria]]l cell, from which it may derive.]]

Mitochondria are organelles that synthesize the energy-carrying molecule [[Adenosine triphosphate|ATP]] for the cell by [[metabolism|metabolizing]] carbon-based [[macromolecule]]s.<ref>{{Cite web |url=https://www.nature.com/scitable/topicpage/mitochondria-14053590 |title=Mitochondria, Cell Energy, ATP Synthase: Learn Science at Scitable |website=www.nature.com |access-date=24 March 2019}}</ref> The presence of [[DNA]] in mitochondria and proteins, derived from [[Mitochondrial DNA|mtDNA]], suggest that this organelle may have been a [[prokaryote]] prior to its integration into the proto-[[eukaryote]].<ref name=":0">{{cite journal |last=Gruber |first=A. |title=What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts |journal=Microbial Cell |volume=6 |issue=2 |pages=123–133 |date=January 2019 |pmid=30740457 |pmc=6364258 |doi=10.15698/mic2019.02.668 }}</ref> 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.<ref name=":0"/> The [[endomembrane system]] and [[Nuclear envelope|nuclear membrane]] were hypothesized to have derived from the [[Proto-mitochondrion|protomitochondria]].<ref name=":2">{{cite journal |last1=Gould |first1=Sven B. |last2=Garg |first2=Sriram G. |last3=Martin |first3=William F. |title=Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System |journal=Trends in Microbiology |volume=24 |issue=7 |pages=525–534 |date=July 2016 |pmid=27040918 |doi=10.1016/j.tim.2016.03.005 }}</ref><ref name=":3">{{cite journal |last1=Martin |first1=William F.|last2=Garg |first2=Sriram |last3=Zimorski |first3=Verena |title=Endosymbiotic theories for eukaryote origin |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=370 |issue=1678 |pages=20140330 |date=September 2015 |pmid=26323761 |pmc=4571569 |doi=10.1098/rstb.2014.0330 }}</ref><ref>{{cite journal |last1=Garavís |first1=Miguel |last2=González |first2=Carlos |last3=Villasante |first3=Alfredo |title=On the origin of the eukaryotic chromosome: the role of noncanonical DNA structures in telomere evolution |journal=Genome Biology and Evolution |volume=5 |issue=6 |pages=1142–50 |date=June 2013 |pmid=23699225 |pmc=3698924 |doi=10.1093/gbe/evt079 }}</ref>

=== Nuclear membrane ===

The presence of a nucleus is one major difference between eukaryotes and [[prokaryote]]s.<ref>{{Cite web |url=https://www.nature.com/scitable/content/typical-prokaryotic-left-and-eukaryotic-right-cells-14665031 |title=Typical prokaryotic (left) and eukaryotic (right) cells: Learn Science at Scitable |website=www.nature.com |access-date=2019-03-24}}</ref> Some conserved [[nuclear protein]]s between eukaryotes and prokaryotes suggest that these two types had a common ancestor.<ref>{{cite journal |last1=Devos |first1=Damien P. |last2=Gräf |first2=Ralph |last3=Field |first3=Mark C. |title=Evolution of the nucleus |journal=[[Current Opinion in Cell Biology]] |volume=28 |pages=8–15 |date=June 2014 |issue=100 |pmid=24508984 |pmc=4071446 |doi=10.1016/j.ceb.2014.01.004 }}</ref> 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]].<ref>{{cite journal |last1=Wilson |first1=Katherine L. |last2=Dawson |first2=Scott C. |title=Evolution: functional evolution of nuclear structure |journal=[[Journal of Cell Biology]] |volume=195 |issue=2 |pages=171–81 |date=October 2011 |pmid=22006947 |pmc=3198171 |doi=10.1083/jcb.201103171 }}</ref>
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.<ref name=":3"/> Digesting engulfed cells without energy-producing mitochondria would have been challenging for the host cell.<ref name=":2"/> On this view, membrane-bound bubbles or [[Vesicle (biology and chemistry)|vesicles]] leaving the protomitochondria may have formed the nuclear envelope.<ref name=":2"/>

The process of symbiogenesis by which the early [[eukaryote|eukaryotic cell]] integrated the proto-[[mitochondrion]] likely included protection of the [[archaea]]l host [[genome]] from the release of [[reactive oxygen species]]. These would have been formed during [[oxidative phosphorylation]] and ATP production by the proto-mitochondrion. The [[nuclear envelope|nuclear membrane]] may have evolved as an adaptive innovation for protecting against nuclear genome [[DNA damage (naturally occurring)|DNA damage]] caused by reactive oxygen species.<ref>{{cite book |last1=Bernstein |first1=H. |last2=Bernstein |first2=C. |chapter=Sexual communication in archaea, the precursor to meiosis |pages=103–117 |title=Biocommunication of Archaea |editor=Witzany, G. |date=2017 |publisher=Springer International Publishing |isbn=978-3-319-65535-2 |doi=10.1007/978-3-319-65536-9 |s2cid=26593032 }}</ref> Substantial transfer of genes from the ancestral proto-mitochondrial genome to the nuclear genome likely occurred during early eukaryotic evolution.<ref name="pmid12893934">{{cite journal |last1=Gabaldón |first1=T. |last2=Huynen |first2=M. A. |title=Reconstruction of the proto-mitochondrial metabolism |journal=Science |volume=301 |issue=5633 |pages=609 |date=August 2003 |pmid=12893934 |doi=10.1126/science.1085463 |s2cid=28868747 }}</ref> 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 ===

[[File:Endomembrane system diagram en.svg|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.<ref>{{cite journal |last1=Liashkovich |first1=Ivan |last2=Shahin |first2=Victor |title=Functional implication of the common evolutionary origin of nuclear pore complex and endomembrane management systems |journal=[[Seminars in Cell and Developmental Biology]] |volume=68 |pages=10–17 |date=August 2017 |pmid=28473267 |doi=10.1016/j.semcdb.2017.04.006 }}</ref> These vesicles also share similar membrane proteins with the organelle they originated from or are traveling towards.<ref name="Howe2008" /> 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.<ref name=":2"/> After the early prokaryote was consumed by a proto-eukaryote, the prokaryote would have continued to produce vesicles that accumulated within the cell.<ref name=":2"/> Interaction of internal components of vesicles may have led to the [[endoplasmic reticulum]] and the [[Golgi apparatus]], both being parts of the endomembrane system.<ref name=":2"/>

=== Cytoplasm ===

The syntrophy hypothesis, proposed by López-García and Moreira around the year 2000, suggested that eukaryotes arose by combining the metabolic capabilities of an archaean, a fermenting deltaproteobacterium, and a methanotrophic alphaproteobacterium which became the mitochondrion. In 2020, the same team updated their syntrophy proposal to cover an [[Asgard (Archaea)|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.<ref name="López-García Moreira 2020">{{cite journal | last1=López-García | first1=Purificación | last2=Moreira | first2=David | title=The Syntrophy hypothesis for the origin of eukaryotes revisited | journal=Nature Microbiology | volume=5 | issue=5 | date=2020-04-27 | issn=2058-5276 | doi=10.1038/s41564-020-0710-4 | pages=655–667| pmid=32341569 | s2cid=81678433 | url=https://hal.archives-ouvertes.fr/hal-02988531/file/Final_submitted_ms.pdf }}</ref>

=== 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 [[acritarch]]s from the 1.631 [[Gya (unit)|Gya]] Deonar Formation of India.<ref>{{Cite journal |last=Prasad |first=Pijai |date=August 2005 |title=Organic-walled microfossils from the Proterozoic Vindhyan Supergroup of Son Valley, Madhya Pradesh, India |url=http://14.139.63.228:8080/pbrep/bitstream/123456789/1084/1/PbV54_13.pdf |journal=Paleobotanist |volume=54 }}</ref> These fossils can still be identified as derived post-nuclear eukaryotes with a sophisticated, morphology-generating [[cytoskeleton]] sustained by mitochondria.<ref>{{Cite journal |last=Butterfield |first=Nicholas J. |date=2014-11-26 |title=Early evolution of the Eukaryota |journal=Palaeontology |volume=58 |issue=1 |pages=5–17 |doi=10.1111/pala.12139|doi-access=free }}</ref> 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.<ref>{{cite journal |last1=Parfrey |first1=Laura Wegener |last2=Lahr |first2=Daniel J. G. |last3=Knoll |first3=Andrew H. |last4=Katz |first4=Laura A. |title=Estimating the timing of early eukaryotic diversification with multigene molecular clocks |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=108 |issue=33 |pages=13624–9 |date=August 2011 |pmid=21810989 |pmc=3158185 |doi=10.1073/pnas.1110633108 |bibcode=2011PNAS..10813624P |doi-access=free }}</ref> A 2.3 Gya estimate<ref>{{cite journal |last1=Hedges |first1=S. Blair |last2=Blair |first2=Jaime E. |last3=Venturi |first3=Maria L. |last4=Shoe |first4=Jason L. |title=A molecular timescale of eukaryote evolution and the rise of complex multicellular life |journal=BMC Evolutionary Biology |volume=4 |pages=2 |date=January 2004 |pmid=15005799 |pmc=341452 |doi=10.1186/1471-2148-4-2 |doi-access=free }}</ref> 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.<ref>{{cite journal |last1=Gross |first1=Jeferson |last2=Bhattacharya |first2=Debashish |title=Uniting sex and eukaryote origins in an emerging oxygenic world |journal=Biology Direct |volume=5 |pages=53 |date=August 2010 |pmid=20731852 |pmc=2933680 |doi=10.1186/1745-6150-5-53 |doi-access=free }}</ref> Alternatively, the Great Oxidation Event might be a consequence of eukaryogenesis, and its impact on the export and burial of organic carbon.<ref>{{Cite journal |last=Butterfield |first=Nicholas J. |date=1997 |title=Plankton ecology and the Proterozoic-Phanerozoic transition |journal=Paleobiology |volume=23 |issue=2 |pages=247–262 |doi=10.1017/S009483730001681X|bibcode=1997Pbio...23..247B |s2cid=140642074 }}</ref>