Editing Chloroplast (section)

==== Chloroplast genome reduction and gene transfer ====

Over time, many parts of the chloroplast genome were transferred to the [[nuclear genome]] of the host,<ref name="Dann-2002" /><ref name="Clegg-1994" /><ref>{{cite journal | vauthors=Huang CY, Ayliffe MA, Timmis JN | title=Direct measurement of the transfer rate of chloroplast DNA into the nucleus | journal=Nature | volume=422 | issue=6927 | pages=72–6 | date=March 2003 | pmid=12594458 | doi=10.1038/nature01435 | bibcode=2003Natur.422...72H | s2cid=4319507 }}</ref> a process called ''[[endosymbiotic gene transfer]]''. As a result, the chloroplast genome is heavily [[genome reduction|reduced]] compared to that of free-living cyanobacteria. Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more than 1500 genes in their genome.<ref name="Martin-2002">{{cite journal | vauthors=Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D | display-authors=6 | title=Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=99 | issue=19 | pages=12246–51 | date=September 2002 | pmid=12218172 | pmc=129430 | doi=10.1073/pnas.182432999 | bibcode=2002PNAS...9912246M | doi-access=free }}</ref> Recently, a plastid without a genome was found, demonstrating chloroplasts can lose their genome during endosymbiotic the gene transfer process.<ref>{{cite journal | vauthors=Smith DR, Lee RW | title=A plastid without a genome: evidence from the nonphotosynthetic green algal genus Polytomella | journal=Plant Physiology | volume=164 | issue=4 | pages=1812–9 | date=April 2014 | pmid=24563281 | pmc=3982744 | doi=10.1104/pp.113.233718 }}</ref>

Endosymbiotic gene transfer is how we know about the [[#Secondary and tertiary endosymbiosis|lost chloroplasts]] in many CASH lineages. Even if a chloroplast is eventually lost, the genes it donated to the former host's nucleus persist, providing evidence for the lost chloroplast's existence. For example, while [[diatoms]] (a [[heterokontophyte]]) now have a [[red algal derived chloroplast]], the presence of many [[green algal]] genes in the diatom nucleus provide evidence that the diatom ancestor had a [[green algal derived chloroplast]] at some point, which was subsequently replaced by the red chloroplast.<ref name="Moustafa-2009" />

In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast,<ref name="Nowack-2011" /> up to 18% in ''[[Arabidopsis]]'', corresponding to about 4,500 protein-coding genes.<ref name="Archibald-2006">{{cite journal | vauthors=Archibald JM | title=Algal genomics: exploring the imprint of endosymbiosis | journal=Current Biology | volume=16 | issue=24 | pages=R1033-5 | date=December 2006 | pmid=17174910 | doi=10.1016/j.cub.2006.11.008 | doi-access=free | bibcode=2006CBio...16R1033A }}</ref> There have been a few recent transfers of genes from the chloroplast DNA to the nuclear genome in land plants.<ref name="Clegg-1994" />

Of the approximately 3000 proteins found in chloroplasts, some 95% of them are encoded by nuclear genes. Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome. As a result, [[protein synthesis]] must be coordinated between the chloroplast and the nucleus. The chloroplast is mostly under nuclear control, though chloroplasts can also give out signals regulating [[gene expression]] in the nucleus, called ''[[retrograde signaling]]''.<ref name="Koussevitzky-2007">{{cite journal|vauthors= Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, Surpin M, Lim J, Mittler R, Chory J|display-authors=6|title=Signals from chloroplasts converge to regulate nuclear gene expression|journal=Science|volume=316|issue=5825|pages=715–9|date=May 2007|pmid= 17395793|doi= 10.1126/science.1140516|bibcode= 2007Sci...316..715K|s2cid=245901639}}
* {{cite magazine |author=Bob Grant |date=1 April 2009 |title=Communicating with chloroplasts |magazine=The Scientist |url=https://www.the-scientist.com/hot-paper/communicating-with-chloroplasts-44253}}</ref> Recent research indicates that parts of the retrograde signaling network once considered characteristic for land plants emerged already in an algal progenitor,<ref>{{Cite journal |last1=de Vries |first1=Jan |last2=Curtis |first2=Bruce A. |last3=Gould |first3=Sven B. |last4=Archibald |first4=John M. |date=10 April 2018 |title=Embryophyte stress signaling evolved in the algal progenitors of land plants |journal=Proceedings of the National Academy of Sciences |language=en |volume=115 |issue=15 |pages=E3471–E3480 |doi=10.1073/pnas.1719230115 |issn=0027-8424 |pmc=5899452 |pmid=29581286 |bibcode=2018PNAS..115E3471D |doi-access=free }}</ref><ref>{{Cite journal |last1=Nishiyama |first1=Tomoaki |last2=Sakayama |first2=Hidetoshi |last3=de Vries |first3=Jan |last4=Buschmann |first4=Henrik |last5=Saint-Marcoux |first5=Denis |last6=Ullrich |first6=Kristian K. |last7=Haas |first7=Fabian B. |last8=Vanderstraeten |first8=Lisa |last9=Becker |first9=Dirk |last10=Lang |first10=Daniel |last11=Vosolsobě |first11=Stanislav |last12=Rombauts |first12=Stephane |last13=Wilhelmsson |first13=Per K.I. |last14=Janitza |first14=Philipp |last15=Kern |first15=Ramona |date=July 2018 |title=The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization |journal=Cell |language=en |volume=174 |issue=2 |pages=448–464.e24 |doi=10.1016/j.cell.2018.06.033|pmid=30007417 |s2cid=206569169 |doi-access=free }}</ref><ref>{{Cite journal |last1=Zhao |first1=Chenchen |last2=Wang |first2=Yuanyuan |last3=Chan |first3=Kai Xun |last4=Marchant |first4=D. Blaine |last5=Franks |first5=Peter J. |last6=Randall |first6=David |last7=Tee |first7=Estee E. |last8=Chen |first8=Guang |last9=Ramesh |first9=Sunita |last10=Phua |first10=Su Yin |last11=Zhang |first11=Ben |last12=Hills |first12=Adrian |last13=Dai |first13=Fei |last14=Xue |first14=Dawei |last15=Gilliham |first15=Matthew |date=12 March 2019 |title=Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land |journal=Proceedings of the National Academy of Sciences |language=en |volume=116 |issue=11 |pages=5015–5020 |doi=10.1073/pnas.1812092116 |issn=0027-8424 |pmc=6421419 |pmid=30804180 |bibcode=2019PNAS..116.5015Z |doi-access=free }}</ref> integrating into co-expressed cohorts of genes in the closest algal relatives of land plants.<ref>{{Cite journal |last1=Dadras |first1=Armin |last2=Fürst-Jansen |first2=Janine M. R. |last3=Darienko |first3=Tatyana |last4=Krone |first4=Denis |last5=Scholz |first5=Patricia |last6=Sun |first6=Siqi |last7=Herrfurth |first7=Cornelia |last8=Rieseberg |first8=Tim P. |last9=Irisarri |first9=Iker |last10=Steinkamp |first10=Rasmus |last11=Hansen |first11=Maike |last12=Buschmann |first12=Henrik |last13=Valerius |first13=Oliver |last14=Braus |first14=Gerhard H. |last15=Hoecker |first15=Ute |date=28 August 2023 |title=Environmental gradients reveal stress hubs pre-dating plant terrestrialization |journal=Nature Plants |volume=9 |issue=9 |pages=1419–1438 |language=en |doi=10.1038/s41477-023-01491-0 |pmid=37640935 |pmc=10505561 |bibcode=2023NatPl...9.1419D |issn=2055-0278}}</ref>