Editing Chloroplast (section)

== Endosymbiotic origin of chloroplasts ==
{{main|Plastid evolution}}
{{See also|Cyanobacteria|Symbiogenesis}}
Chloroplasts are one of many types of organelles in photosynthetic eukaryotic cells. They evolved from [[cyanobacteria]] through a process called [[Symbiogenesis|organellogenesis]].<ref name="Moore-2019">{{cite journal | vauthors=Moore KR, Magnabosco C, Momper L, Gold DA, Bosak T, Fournier GP | title=An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids | language=en | journal=Frontiers in Microbiology | volume=10 | page=1612 | date=2019 | pmid=31354692 | pmc=6640209 | doi=10.3389/fmicb.2019.01612 | doi-access=free }}</ref> Cyanobacteria are a diverse [[phylum]] of [[Gram-negative bacteria|gram-negative]] [[bacteria]] capable of carrying out [[photosynthesis|oxygenic photosynthesis]]. Like chloroplasts, they have [[thylakoid]]s.<ref name="Campbell-2009g">{{cite book |title=Biology |vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |publisher=Benjamin Cummings (Pearson) |year=2009 |isbn=978-0-8053-6844-4 |edition=8th |pages=186–187}}</ref> The thylakoid membranes contain [[photosynthetic pigment]]s, including [[chlorophyll a|chlorophyll ''a'']].<ref name="Kim-2009" /><ref>{{cite journal  | vauthors=Bryant DA, Guglielmi G, de Marsac NT, Castets AM, Cohen-Bazire G |doi=10.1007/BF00446810 |title=The structure of cyanobacterial phycobilisomes: A model |year=1979 |journal=Archives of Microbiology |volume=123 |issue=2 |pages=311–34 |bibcode=1979ArMic.123..113B |s2cid=1589428 }}</ref> This origin of chloroplasts was first suggested by the Russian biologist [[Konstantin Mereschkowski]] in 1905<ref>{{cite journal |author=Mereschkowsky K |author-link=Konstantin Mereschkowski |title= Über Natur und Ursprung der Chromatophoren im Pflanzenreiche |trans-title=About the nature and origin of chromatophores in the vegetable kingdom |language=de|journal= Biol Centralbl|year=1905|volume=25|pages=593–604 |url=https://archive.org/details/cbarchive_51353_bernaturundursprungderchromato1881}}</ref> after [[Andreas Franz Wilhelm Schimper]] observed in 1883 that chloroplasts closely resemble [[cyanobacteria]].<ref name="Schimper-1883" /> Chloroplasts are only found in [[plant]]s, [[algae]],<ref name="Alberts-2002a">{{cite book |last=Alberts|first=Bruce| name-list-style=vanc |title=Molecular biology of the cell|year=2002|publisher=Garland|location=New York [u.a.]|isbn=0-8153-4072-9|url=https://www.ncbi.nlm.nih.gov/books/NBK26819/|edition=4.}}</ref> and some species of the [[amoeba|amoeboid]] ''[[Paulinella]]''.<ref name="Gabr-2020">{{cite journal |vauthors=Gabr A, Grossman AR, Bhattacharya D |title=Paulinella, a model for understanding plastid primary endosymbiosis |journal=J Phycol |volume=56 |issue=4 |pages=837–843 |date=August 2020 |pmid=32289879 |pmc=7734844 |doi=10.1111/jpy.13003 |bibcode=2020JPcgy..56..837G |url=}}</ref>

[[Mitochondrion|Mitochondria]] are thought to have come from a similar [[endosymbiosis]] event, where an [[Aerobic organism|aerobic]] [[prokaryote]] was engulfed.<ref name="Campbell-2009c">{{cite book |title=Biology |vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |publisher=Benjamin Cummings (Pearson) |year=2009 |isbn=978-0-8053-6844-4 |edition=8th |page=516}}</ref> 

=== Primary endosymbiosis ===

{{Plain image with caption|Chloroplast endosymbiosis simple.svg|'''Primary endosymbiosis'''<br />A eukaryote with [[Mitochondrion|mitochondria]] engulfed a [[cyanobacterium]] in an event of [[Serial endosymbiosis|serial]] primary endosymbiosis, creating a [[Archæplastida|lineage]] of cells with both organelles.<ref name="Campbell-2009c" />|400px|right|bottom|triangle|#1abc31}}

Approximately two{{Nbsp}}billion years ago,<ref name="Milo" /><ref name="Sánchez-Baracaldo-2017">
{{cite journal | vauthors=Sánchez-Baracaldo P, Raven JA, Pisani D, Knoll AH | title=Early photosynthetic eukaryotes inhabited low-salinity habitats | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=114 | issue=37 | pages=E7737–E7745 | date=September 2017 | pmid=28808007 | pmc=5603991 | doi=10.1073/pnas.1620089114 | bibcode=2017PNAS..114E7737S | doi-access=free }}</ref><ref>{{Cite journal |last1=Falcón |first1=Luisa I |last2=Magallón |first2=Susana |last3=Castillo |first3=Amanda |date=4 March 2010 |title=Dating the cyanobacterial ancestor of the chloroplast |url=https://academic.oup.com/ismej/article/4/6/777/7588052 |journal=The ISME Journal |language=en |volume=4 |issue=6 |pages=777–783 |doi=10.1038/ismej.2010.2 |pmid=20200567 |bibcode=2010ISMEJ...4..777F |issn=1751-7362}}</ref> a free-living [[cyanobacterium]] entered an early [[eukaryotic]] cell, either as food or as an internal [[parasite]],<ref name="Campbell-2009c" /> but managed to escape the [[phagocytic vacuole]] it was contained in and persist inside the cell.<ref name="Kim-2009" /> This event is called ''[[endosymbiosis]]'', or "cell living inside another cell with a mutual benefit for both". The external cell is commonly referred to as the ''host'' while the internal cell is called the ''endosymbiont''.<ref name="Campbell-2009c" /> The engulfed cyanobacteria provided an advantage to the host by providing sugar from photosynthesis.<ref name="Campbell-2009c" /> Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to the [[nuclear genome|nucleus]] of the host.<ref name="Nakayama-2012">{{cite journal |vauthors=Nakayama T, Archibald JM |date=April 2012 |title=Evolving a photosynthetic organelle |journal=BMC Biology |volume=10 |issue=1 |page=35 |doi=10.1186/1741-7007-10-35 |pmc=3337241 |pmid=22531210 |doi-access=free}}</ref> Some of the cyanobacterial proteins were then synthesized by host cell and imported back into the chloroplast (formerly the cyanobacterium), allowing the host to control the chloroplast.<ref name="Nakayama-2012" /><ref name="McFadden-2001" />

Chloroplasts which can be traced back directly to a cyanobacterial ancestor (i.e. without a subsequent endosymbiotic event) are known as '''''primary plastids''''' ("[[plastid]]" in this context means almost the same thing as chloroplast<ref name="Campbell-2009c" />).<ref name="Wise-2006b" /> Chloroplasts that can be traced back to another photosynthetic eukaryotic endosymbiont are called '''''secondary plastids''''' or '''''tertiary plastids''''' (discussed below).

Whether primary chloroplasts came from a single endosymbiotic event or multiple independent engulfments across various eukaryotic lineages was long debated. It is now generally held that with one exception (the amoeboid ''Paulinella chromatophora''), chloroplasts arose from a single endosymbiotic event around two{{Nbsp}}billion years ago and these chloroplasts all share [[monophyly|a single ancestor]].<ref name="Sánchez-Baracaldo-2017" /> It has been proposed this the closest living relative of the ancestral engulfed cyanobacterium is ''[[Gloeomargarita lithophora]].''<ref>{{cite journal |vauthors=Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D |date=February 2017 |title=An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids |journal=Current Biology |volume=27 |issue=3 |pages=386–391 |bibcode=2017CBio...27..386P |doi=10.1016/j.cub.2016.11.056 |pmc=5650054 |pmid=28132810}}</ref><ref>{{cite journal |vauthors=de Vries J, Archibald JM |date=February 2017 |title=Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium? |journal=Current Biology |volume=27 |issue=3 |pages=R103–R105 |bibcode=2017CBio...27.R103D |doi=10.1016/j.cub.2016.12.006 |pmid=28171752 |doi-access=free}}</ref><ref name="López-García-2017">{{cite journal |vauthors=López-García P, Eme L, Moreira D |date=December 2017 |title=Symbiosis in eukaryotic evolution |journal=Journal of Theoretical Biology |volume=434 |pages=20–33 |bibcode=2017JThBi.434...20L |doi=10.1016/j.jtbi.2017.02.031 |pmc=5638015 |pmid=28254477}}</ref> Separately, somewhere about 90–140&nbsp;million years ago, this process happened again in the [[amoeboid]] ''[[Paulinella]]'' with a cyanobacterium in the genus ''[[Prochlorococcus]]''. This independently evolved chloroplast is often called a ''chromatophore'' instead of a chloroplast.<ref name="Macorano-2021">{{Cite journal |last1=Macorano |first1=Luis |last2=Nowack |first2=Eva C.M. |date=13 September 2021 |title=Paulinella chromatophora |url=https://linkinghub.elsevier.com/retrieve/pii/S0960982221009830 |journal=Current Biology |language=en |volume=31 |issue=17 |pages=R1024–R1026 |doi=10.1016/j.cub.2021.07.028|pmid=34520707 |bibcode=2021CBio...31R1024M }}</ref><ref group="Note" name=":0">Not to be confused with [[chromatophore]]—the pigmented cells in some animals—or [[Chromatophore (bacteria)|chromatophore]]—the membrane associated vesicle in some bacteria.</ref>

Chloroplasts are believed to have arisen after [[Mitochondrion|mitochondria]], since all [[eukaryote]]s contain mitochondria, but not all have chloroplasts.<ref name="Campbell-2009c" /><ref>{{cite journal |vauthors=Archibald JM |date=January 2009 |title=The puzzle of plastid evolution |journal=Current Biology |volume=19 |issue=2 |pages=R81-8 |bibcode=2009CBio...19..R81A |doi=10.1016/j.cub.2008.11.067 |pmid=19174147 |s2cid=51989 |doi-access=free}}</ref> This is called ''[[serial endosymbiosis]]''—where an early eukaryote engulfed the [[mitochondrion]] ancestor, and then descendants of it then engulfed the chloroplast ancestor, creating a cell with both chloroplasts and mitochondria.<ref name="Campbell-2009c" />

=== Secondary and tertiary endosymbiosis ===

{{plain image with caption|File:Chloroplast secondary endosymbiosis.svg|Secondary endosymbiosis consisted of a [[eukaryote|eukaryotic]] [[Algae|alga]] being engulfed by another eukaryote, forming a chloroplast with three or four membranes.|600px|right|bottom|triangle|#71d7ff}}

Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga with a primary chloroplast. These chloroplasts are known as '''secondary plastids'''.<ref name="Wise-2006b" />

As a result of the secondary endosymbiotic event, secondary chloroplasts have additional membranes outside of the original two in primary chloroplasts.<ref name="Keeling-2004">{{cite journal |vauthors=Keeling PJ |date=October 2004 |title=Diversity and evolutionary history of plastids and their hosts |journal=American Journal of Botany |volume=91 |issue=10 |pages=1481–93 |doi=10.3732/ajb.91.10.1481 |pmid=21652304 |s2cid=17522125 |doi-access=free}}</ref> In secondary plastids, typically only the chloroplast, and sometimes its [[cell membrane]] and [[Cell nucleus|nucleus]] remain, forming a chloroplast with three or four membranes<ref name="Chaal-2005">{{cite journal |vauthors=Chaal BK, Green BR |date=February 2005 |title=Protein import pathways in 'complex' chloroplasts derived from secondary endosymbiosis involving a red algal ancestor |journal=Plant Molecular Biology |volume=57 |issue=3 |pages=333–42 |doi=10.1007/s11103-004-7848-y |pmid=15830125 |s2cid=22619029}}</ref>—the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and the [[phagosomal vacuole]] from the host's cell membrane.<ref name="Keeling-2004" />

The genes in the phagocytosed eukaryote's nucleus are often transferred to the secondary host's nucleus.<ref name="Keeling-2004" /> [[Cryptomonad]]s and [[chlorarachniophyte]]s retain the phagocytosed eukaryote's nucleus, an object called a [[nucleomorph]],<ref name="Keeling-2004" /> located between the second and third membranes of the chloroplast.<ref name="Kim-2009" /><ref name="McFadden-2001" />

All secondary chloroplasts come from [[green algae|green]] and [[red algae]]. No secondary chloroplasts from [[glaucophytes]] have been observed, probably because glaucophytes are relatively rare in nature, making them less likely to have been taken up by another eukaryote.<ref name="Keeling-2004" />

Still other organisms, including the dinoflagellates ''[[Karlodinium]]'' and ''[[Karenia (dinoflagellate)|Karenia]],'' obtained chloroplasts by engulfing an organism with a secondary plastid. These are called '''tertiary plastids'''.<ref name="Wise-2006b" />
[[File:Chloroplast Cladogram.svg|alt=Cladogram of chloroplast evolution|center|thumb|800x800px|'''Possible cladogram of chloroplast evolution'''<ref name="Keeling-2004" /><ref name="McFadden-2004">{{cite journal |last1=McFadden |first1=Geoffrey I. |last2=Van Dooren |first2=Giel G. |date=2004 |title=Evolution: Red Algal Genome Affirms a Common Origin of All Plastids |journal=Current Biology |volume=14 |issue=13 |pages=R514–R516 |bibcode=2004CBio...14.R514M |doi=10.1016/j.cub.2004.06.041 |pmid=15242632}}</ref><ref name="Keeling-2010" /> Circles represent [[endosymbiotic]] events. For clarity, [[dinophyte]] tertiary endosymbioses and many nonphotosynthetic lineages have been omitted.
----<small><sup>'''a'''</sup> It is now established that [[Chromalveolata]] is [[paraphyletic]] to [[Rhizaria]].<ref name="Keeling-2010" /></small>]]