Editing Symbiogenesis (section)

=== Free-living ancestors ===

[[Alphaproteobacteria]] were formerly thought to be the free-living organisms most closely related to mitochondria.<ref name="Timmis2004">{{cite journal |last1=Timmis |first1=Jeremy N. |last2=Ayliffe |first2=Michael A. |last3=Huang |first3=Chun Y. |last4=Martin |first4=William |author4-link=William F. Martin |title=Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes |journal=[[Nature Reviews Genetics]] |volume=5 |issue=2 |year=2004 |doi=10.1038/nrg1271 |pages=123–135|pmid=14735123 |s2cid=2385111 }}</ref> Later research indicates that mitochondria are most closely related to [[Pelagibacterales]] bacteria, in particular, those in the SAR11 clade.<ref>{{cite web |url=https://www.sciencedaily.com/releases/2011/07/110725190046.htm |title=Mitochondria Share an Ancestor With SAR11, a Globally Significant Marine Microbe |date=July 25, 2011 |website=ScienceDaily |access-date=26 July 2011}}</ref><ref>{{cite journal |last1=Thrash |first1=J. Cameron |last2=Boyd |first2=Alex |last3=Huggett |first3=Megan J. |last4=Grote |first4=Jana |last5=Carini |first5=Paul |last6=Yoder |first6=Ryan J. |last7=Robbertse |first7=Barbara |last8=Spatafora |first8=Joseph W. |last9=Rappé |first9=Michael S. |last10=Giovannoni |first10=Stephen J. |display-authors=3 |title=Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade |journal=Scientific Reports |volume=1 |issue=1 |date=14 June 2011 |page=13 |doi=10.1038/srep00013 |pmid=22355532 |pmc=3216501 |bibcode=2011NatSR...1...13T }}</ref> 

[[Diazotrophs|Nitrogen-fixing]] filamentous [[cyanobacteria]] are the free-living organisms most closely related to plastids.<ref name="Timmis2004"/><ref name="Deusch">{{cite journal |last1=Deusch |first1=O. |last2=Landan |first2=G. |last3=Roettger |first3=M. |last4=Gruenheit |first4=N. |last5=Kowallik |first5=K. V. |last6=Allen |first6=J. F. |last7=Martin |first7=W. |last8=Dagan |first8=T.  |display-authors=3 |title=Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor |journal=Molecular Biology and Evolution |volume=25 |issue=4 |date=14 February 2008 |doi=10.1093/molbev/msn022 |pages=748–761|pmid=18222943 }}</ref><ref>{{cite journal |last1=Ochoa de Alda |first1=Jesús A. G. |last2=Esteban |first2=Rocío |last3=Diago |first3=María Luz |last4=Houmard |first4=Jean |display-authors=3 |title=The plastid ancestor originated among one of the major cyanobacterial lineages |journal=Nature Communications |volume=5 |issue=1 |date=15 September 2014 |page=4937 |doi=10.1038/ncomms5937 |pmid=25222494 |bibcode=2014NatCo...5.4937O |doi-access=free }}</ref>

Both cyanobacteria and alphaproteobacteria maintain a large (>6{{nbsp}}[[Megabase|Mb]]) genome encoding thousands of proteins.<ref name="Timmis2004"/> [[Plastid]]s and [[mitochondria]] exhibit a dramatic reduction in genome size when compared with their bacterial relatives.<ref name="Timmis2004"/> Chloroplast genomes in photosynthetic organisms are normally 120–200{{nbsp}}kb<ref name="LilaKoumandou2004">{{cite journal |last1=Lila Koumandou |first1=V. |last2=Nisbet |first2=R. Ellen R. |last3=Barbrook |first3=Adrian C. |last4=Howe |first4=Christopher J. |display-authors=3 |title=Dinoflagellate chloroplasts—where have all the genes gone? |journal=[[Trends in Genetics]] |volume=20 |issue=5 |pages=261–267 |date=May 2004 |pmid=15109781 |doi=10.1016/j.tig.2004.03.008 }}</ref> encoding 20–200 proteins<ref name="Timmis2004"/> and mitochondrial genomes in humans are approximately 16{{nbsp}}kb and encode 37 genes, 13 of which are proteins.<ref name="Taanman1999">{{cite journal |last=Taanman |first=J. W. |title=The mitochondrial genome: structure, transcription, translation and replication |journal=Biochimica et Biophysica Acta (BBA) - Bioenergetics |volume=1410 |issue=2 |pages=103–23 |date=February 1999 |pmid=10076021 |doi=10.1016/S0005-2728(98)00161-3 |doi-access=free }}</ref> Using the example of the freshwater [[Amoeba|amoeboid]], however, ''[[Paulinella]] chromatophora'', which contains [[chromatophore]]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 [[Cell division|own division]].<ref name="Keeling 2008"/> Nowack and her colleagues gene sequenced the chromatophore (1.02{{nbsp}}Mb) and found that only 867 proteins were encoded by these photosynthetic cells. Comparisons with their closest free living cyanobacteria of the genus ''[[Synechococcus]]'' (having a genome size 3{{nbsp}}Mb, with 3300 genes) revealed that chromatophores had undergone a drastic genome shrinkage. Chromatophores contained genes that were accountable for [[photosynthesis]] 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]] of photosynthetic organelles.<ref>{{cite journal |last1=Nowack |first1=E. C. |last2=Melkonian |first2=M. |last3=Glockner |first3=G. |title=Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes |journal=Current Biology |volume=18 |issue=6 |pages=410–8 |date=March 2008 |pmid=18356055 |doi=10.1016/j.cub.2008.02.051 |s2cid=15929741 |doi-access=free |bibcode=2008CBio...18..410N }}</ref>

The loss of genetic autonomy, that is, the loss of many genes from endosymbionts, occurred very early in evolutionary time.<ref name="Barbrook2006">{{cite journal |last1=Barbrook |first1=Adrian C. |last2=Howe |first2=Christopher J. |last3=Purton |first3=Saul |title=Why are plastid genomes retained in non-photosynthetic organisms? |journal=Trends in Plant Science |volume=11 |issue=2 |pages=101–8 |date=February 2006 |pmid=16406301 |doi=10.1016/j.tplants.2005.12.004 }}</ref> 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,<ref name="Barbrook2006"/> in which genes that are already represented in the nucleus are eventually lost. The second is the [[horizontal gene transfer|transfer]] of genes to the nucleus, while the third is that genes remain in the organelle that was once an organism.<ref name="Timmis2004"/><ref name="Barbrook2006"/><ref name="Leister2005">{{cite journal |last=Leister |first=D. |title=Origin, evolution and genetic effects of nuclear insertions of organelle DNA |journal=Trends in Genetics |volume=21 |issue=12 |pages=655–63 |date=December 2005 |pmid=16216380 |doi=10.1016/j.tig.2005.09.004 |url=http://edoc.mpg.de/277780 |hdl=11858/00-001M-0000-0012-3B56-7 |hdl-access=free }}</ref><ref name="Keeling2004">{{cite journal |last=Keeling |first=P. J. |title=Diversity and evolutionary history of plastids and their hosts |journal=American Journal of Botany |volume=91 |issue=10 |pages=1481–93 |date=October 2004 |pmid=21652304 |doi=10.3732/ajb.91.10.1481 |doi-access=free }}</ref><ref name="Archibald2009">{{cite journal |last=Archibald |first=J. M. |title=The puzzle of plastid evolution |journal=Current Biology |volume=19 |issue=2 |pages=R81–R88 |date=January 2009 |pmid=19174147 |doi=10.1016/j.cub.2008.11.067 |s2cid=51989 |doi-access=free |bibcode=2009CBio...19..R81A }}</ref> The loss of autonomy and integration of the endosymbiont with its host can be primarily attributed to nuclear gene transfer.<ref name="Archibald2009"/> As organelle genomes have been greatly reduced over evolutionary time, [[nuclear gene]]s have expanded and become more complex.<ref name="Timmis2004"/> As a result, many plastid and mitochondrial processes are driven by nuclear encoded gene products.<ref name="Timmis2004"/> In addition, many nuclear genes originating from endosymbionts have acquired novel functions unrelated to their organelles.<ref name="Timmis2004"/><ref name="Archibald2009"/>