# Plastid DNA

> Mediated Wiki article. Canonical URL: https://mediated.wiki/source/Plastid_DNA
> Markdown URL: https://mediated.wiki/source/Plastid_DNA.md
> Source: https://en.wikipedia.org/wiki/Plastid_DNA
> Source revision: 1342675326
> License: Creative Commons Attribution-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/)

{{Short description|DNA located in cellular organelles called chloroplasts}}
{{Chloroplast DNA|caption='''Chloroplast DNA''' Interactive gene map of chloroplast DNA from ''[Nicotiana tabacum](/source/Nicotiana_tabacum)''. Segments with labels on the inside reside on the B strand of [DNA](/source/DNA), segments with labels on the outside are on the A strand. Notches indicate [introns](/source/introns).}}
'''Plastid DNA''' ('''ptDNA'''), also known as '''chloroplast DNA''' ('''cpDNA''' or '''ctDNA'''<ref name="PlantBiochemistry"/>) in photosynthetic organisms, is the [DNA](/source/DNA) located in [chloroplast](/source/chloroplast)s, which are [photosynthetic](/source/Photosynthesis) [organelle](/source/organelle)s located within the [cells](/source/Cell_(biology)) of some [eukaryotic](/source/Eukaryote) organisms, as well as some reduced plastids, such as [apicoplast](/source/apicoplast)s.<ref name="CcptDNA">{{cite journal|author=Hunter E, Paight CJ, Lane CE|date=2020-12-01|title=Metabolic contributions of an alphaproteobacterial endosymbiont in the apicomplexan ''Cardiosporidium cionae''|journal=Front Microbiol|volume=11|pp=1–11|doi=10.3389/fmicb.2020.580719|pmc=7737231|pmid=33335517|doi-access=free}}</ref> Chloroplasts, like other types of [plastid](/source/plastid), contain a [genome](/source/genome) separate from that in the cell [nucleus](/source/Cell_nucleus). The existence of chloroplast DNA was identified [biochemically](/source/Biochemistry) in 1959,<ref name="Stocking1959" /> and confirmed by [electron microscopy](/source/Electron_microscope) in 1962.<ref name="Ris1962" /> The discoveries that the chloroplast contains [ribosome](/source/ribosome)s<ref name="Lyttleton1962" /> and performs [protein synthesis](/source/Protein_biosynthesis)<ref name="Heber1962" /> revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast [genome sequences](/source/Genome_sequencing) were published in 1986, ''[Nicotiana tabacum](/source/Nicotiana_tabacum)'' (tobacco) by Sugiura and colleagues and ''[Marchantia polymorpha](/source/Marchantia_polymorpha)'' (liverwort) by Ozeki et al.<ref>{{Cite journal |last1=Shinozaki |first1=K. |last2=Ohme |first2=M. |last3=Tanaka |first3=M. |last4=Wakasugi |first4=T. |last5=Hayashida |first5=N. |last6=Matsubayashi |first6=T. |last7=Zaita |first7=N. |last8=Chunwongse |first8=J. |last9=Obokata |first9=J.|last10=Yamaguchi-Shinozaki|first10=K. |last11=Ohto |first11=C. |date=1986 |title=The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression |journal=The EMBO Journal |volume=5 |issue=9 |pages=2043–2049 |doi=10.1002/j.1460-2075.1986.tb04464.x |pmid=16453699 |pmc=1167080 |issn=0261-4189}}</ref><ref>{{Cite journal |last1=Ohyama |first1=Kanji |last2=Fukuzawa |first2=Hideya |last3=Kohchi |first3=Takayuki |last4=Shirai |first4=Hiromasa |last5=Sano |first5=Tohru |last6=Sano |first6=Satoshi |last7=Umesono |first7=Kazuhiko |last8=Shiki |first8=Yasuhiko |last9=Takeuchi |first9=Masayuki|last10=Chang|first10=Zhen |last11=Aota |first11=Shin-ichi |date=1986 |title=Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA |url=https://www.nature.com/articles/322572a0 |journal=Nature |language=en |volume=322 |issue=6079 |pages=572–574 |doi=10.1038/322572a0 |bibcode=1986Natur.322..572O |s2cid=4311952 |issn=1476-4687|url-access=subscription }}</ref> Since then, [tens of thousands of chloroplast genomes](/source/List_of_sequenced_plastomes) from various species have been [sequenced](/source/DNA_sequencing).

==Molecular structure==
[[File:Plastomap of Arabidopsis thaliana.svg|thumb|400px|The 154 kb chloroplast DNA map of a model flowering plant (''[Arabidopsis thaliana](/source/Arabidopsis_thaliana)'': Brassicaceae) showing genes and inverted repeats.]]

[Chloroplast](/source/Chloroplast) DNAs are circular, and are typically 120,000–170,000 [base pairs](/source/base_pairs) long.<ref name=BioscienceExplained /><ref name=PNAS-RatesofctDNAevolution /><ref name=AmericanJournalofBotany /> They can have a contour length of around 30–60 micrometers, and have a mass of about 80–130 million [dalton](/source/dalton_(unit))s.<ref name=IntroductiontoPlantCellDevelopment-ctDNA-62>{{cite book |last=Burgess |first=Jeremy |name-list-style=vanc |title=An introduction to plant cell development |year=1989 |publisher=Cambridge university press |location=Cambridge |isbn=978-0-521-31611-8 |page=62 |url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA62}}</ref>

Most chloroplasts have their entire chloroplast genome combined into a single large ring, though those of [dinophyte algae](/source/dinophyte_algae) are a notable exception—their genome is broken up into about forty small [plasmids](/source/plasmids), each 2,000–10,000 [base pairs](/source/base_pairs) long.<ref name=Springer-TheChloroplast-18 /> Each minicircle contains one to three genes,<ref name=Springer-TheChloroplast-18 /> but blank plasmids, with no [coding DNA](/source/coding_DNA), have also been found.

Chloroplast DNA has long been thought to have a circular structure, but some evidence suggests that chloroplast DNA more commonly takes a linear shape.<ref name="The Plant Cell—Linear chloroplast DNA">{{cite journal |vauthors=Bendich AJ |title=Circular chloroplast chromosomes: the grand illusion |journal=The Plant Cell |volume=16 |issue=7 |pages=1661–6 |date=July 2004 |pmid=15235123 |pmc=514151 |doi=10.1105/tpc.160771|bibcode=2004PlanC..16.1661B }}</ref> Over 95% of the chloroplast DNA in [corn](/source/corn) chloroplasts has been observed to be in branched linear form rather than individual circles.<ref name=Springer-TheChloroplast-18 />

===Inverted repeats===
Many chloroplast DNAs contain two ''inverted repeats'', which separate a long single copy section (LSC) from a short single copy section (SSC).<ref name=AmericanJournalofBotany>{{cite journal |vauthors=Shaw J, Lickey EB, Schilling EE, Small RL |title=Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III |journal=American Journal of Botany |volume=94 |issue=3 |pages=275–88 |date=March 2007 |pmid=21636401 |doi=10.3732/ajb.94.3.275 |s2cid=30501148}}</ref>

The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 [base pairs](/source/base_pairs) long each.<ref name=Springer-TheChloroplast-18 /> Inverted repeats in plants tend to be at the upper end of this range, each being 20,000–25,000 base pairs long.<ref name=AmericanJournalofBotany /><ref name=PNAS-InvertedRepeats>{{cite journal |vauthors=Kolodner R, Tewari KK |title=Inverted repeats in chloroplast DNA from higher plants |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=76 |issue=1 |pages=41–5 |date=January 1979 |pmid=16592612 |pmc=382872 |doi=10.1073/pnas.76.1.41 |bibcode=1979PNAS...76...41K |doi-access=free}}</ref>
The inverted repeat regions usually contain three [ribosomal RNA](/source/ribosomal_RNA) and two [tRNA](/source/tRNA) genes, but they can be expanded or [reduced](/source/genome_reduction) to contain as few as four or as many as over 150 genes.<ref name=Springer-TheChloroplast-18 />
While a given pair of inverted repeats are rarely completely identical, they are always very similar to each other, apparently resulting from [concerted evolution](/source/concerted_evolution).<ref name=Springer-TheChloroplast-18 />

The inverted repeat regions are highly [conserved](/source/Conserved_sequence) among land plants, and accumulate few mutations.<ref name=AmericanJournalofBotany /><ref name=PNAS-InvertedRepeats /> Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages ([glaucophyta](/source/glaucophyta) and [rhodophyceæ](/source/red_algae)), suggesting that they predate the chloroplast,<ref name=Springer-TheChloroplast-18 /> though some chloroplast DNAs like those of [peas](/source/peas) and a few [red algae](/source/red_algae)<ref name=Springer-TheChloroplast-18 /> have since lost the inverted repeats.<ref name=PNAS-InvertedRepeats /><ref name=Cell-ctDNArearrangement /> Others, like the red alga ''[Porphyra](/source/Porphyra)'' flipped one of its inverted repeats (making them direct repeats).<ref name=Springer-TheChloroplast-18 /> It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast DNAs which have lost some of the inverted repeat segments tend to get rearranged more.<ref name=Cell-ctDNArearrangement>{{cite journal |vauthors=Palmer JD, Thompson WF |title=Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost |journal=Cell |volume=29 |issue=2 |pages=537–50 |date=June 1982 |pmid=6288261 |doi=10.1016/0092-8674(82)90170-2 |s2cid=11571695}}</ref>

===Nucleoids===

In young leaves, each chloroplast contains around 100 copies of its DNA, declining to 15–20 copies in older leaves.<ref name=PlantBiochemistry>{{cite book |title=Plant Biochemistry |edition=3rd |year=2005 |publisher=Academic Press |page=[https://archive.org/details/isbn_9788131200032/page/517 517] |url=https://archive.org/details/isbn_9788131200032 |url-access=registration |quote=number of copies of ctDNA per chloroplast. |isbn=978-0-12-088391-2}}</ref> They are usually packed into [nucleoids](/source/nucleoids) which can contain several identical chloroplast DNA rings. Many nucleoids can be found in each chloroplast.<ref name=IntroductiontoPlantCellDevelopment-ctDNA-62 />

Though chloroplast DNA is not associated with true [histone](/source/histone)s,<ref name=Biology-Campbell&Reece>{{cite book |title=Biology 8th Edition Campbell & Reece |year=2009 |publisher=Benjamin Cummings (Pearson) |page=516}}</ref> in [red algae](/source/red_algae), a histone-like chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast DNA ring into a [nucleoid](/source/nucleoid) has been found.<ref name="TPC-ChloroplastNucleoids">{{cite journal |vauthors=Kobayashi T, Takahara M, Miyagishima SY, Kuroiwa H, Sasaki N, Ohta N, Matsuzaki M, Kuroiwa T |title=Detection and localization of a chloroplast-encoded HU-like protein that organizes chloroplast nucleoids |journal=The Plant Cell |volume=14 |issue=7 |pages=1579–89 |date=July 2002 |pmid=12119376 |pmc=150708 |doi=10.1105/tpc.002717|bibcode=2002PlanC..14.1579K }}</ref>

In primitive [red algae](/source/red_algae), the chloroplast DNA nucleoids are clustered in the center of a chloroplast, while in [green plants](/source/Viridiplantae), the nucleoids are dispersed throughout the [stroma](/source/stroma_(fluid)).<ref name="TPC-ChloroplastNucleoids" />

== Gene content and plastid gene expression ==
{{See also|List of sequenced plastomes|label 1=List of sequenced plastomes}}
More than 33,000 chloroplast genomes have been [sequenced](/source/DNA_sequencing) and are accessible via the NCBI organelle genome database.<ref name="NCBI-Organelle" /> The first chloroplast genomes were sequenced in 1986, from tobacco (''Nicotiana tabacum'')<ref name="Ohyama1986" /> and liverwort (''Marchantia polymorpha'').<ref name="Shinozaki1986" /> Comparison of the gene sequences of the cyanobacteria ''Synechocystis'' to those of the chloroplast genome of ''Arabidopsis'' provided confirmation of the [endosymbiotic](/source/endosymbiont) origin of the chloroplast.<ref name="Kaneko1997" /><ref name="Sato1999" /> It also demonstrated the significant extent of [gene transfer](/source/horizontal_gene_transfer) from the cyanobacterial ancestor to the nuclear genome.

In most plant species, the chloroplast genome encodes approximately 120 genes.<ref name="Daniell2016" /><ref name="Clegg1994" /> The genes primarily encode core components of the photosynthetic machinery and factors involved in their expression and assembly.<ref name="Berry2013" /> Across species of land plants, the set of genes encoded by the chloroplast genome is fairly conserved. This includes four [ribosomal RNAs](/source/ribosomal_RNAs), approximately 30 [tRNAs](/source/tRNAs), 21 [ribosomal proteins](/source/ribosomal_proteins), and 4 subunits of the plastid-encoded [RNA polymerase](/source/RNA_polymerase) complex that are involved in plastid gene expression.<ref name="Berry2013" /> The large [Rubisco](/source/Rubisco) subunit and 28 photosynthetic [thylakoid](/source/thylakoid) proteins are encoded within the chloroplast genome.<ref name="Berry2013" />

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

Over time, many parts of the chloroplast genome were transferred to the [nuclear genome](/source/nuclear_genome) of the host,<ref name=BioscienceExplained /><ref name=PNAS-RatesofctDNAevolution /><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](/source/endosymbiotic_gene_transfer)''.
As a result, the chloroplast genome is heavily [reduced](/source/genome_reduction) 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="PNAS—Cyanobacterial genes in Arabidopsis">{{cite journal |vauthors=Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D |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> The parasitic ''[Pilostyles](/source/Pilostyles)'' have even lost their plastid genes for [tRNA](/source/tRNA).<ref>{{cite journal |doi=10.1093/gbe/evv251 |title=The Plastomes of Two Species in the Endoparasite Genus ''Pilostyles'' (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes |date=2016 |last1=Bellot |first1=Sidonie |last2=Renner |first2=Susanne S. |journal=Genome Biology and Evolution |volume=8 |issue=1 |pages=189–201 |pmid=26660355 |pmc=4758247 }}</ref> Contrarily, there are only a few known instances where genes have been transferred to the chloroplast from various donors, including bacteria.<ref name="MackiewiczBodył2014">{{cite journal |vauthors=Mackiewicz P, Bodył A, Moszczyński K |title=The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome |journal=Mobile Genetic Elements |volume=3 |issue=4 |article-number=e25845 |date=July 2013 |pmid=24195014 |pmc=3812789 |doi=10.4161/mge.25845}}</ref><ref name="LeliaertLopez-Bautista2015">{{cite journal |vauthors=Leliaert F, Lopez-Bautista JM |title=The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin |journal=BMC Genomics |volume=16 |issue=1 |page=204 |date=March 2015 |pmid=25879186 |pmc=4487195 |doi=10.1186/s12864-015-1418-3 |doi-access=free}}</ref><ref name="Robison2018">{{cite journal |vauthors=Robison, TA, Grusz AL, Wolf PG, Mower, JP, Fauskee BD, Sosa K, and Schuettpelz E |title=Mobile Elements Shape Plastome Evolution in Ferns |journal=Genome Biology and Evolution |volume=10 |issue=10 |pages=2669–2571 |date=October 2018 |pmid=30165616 |pmc=6166771 |doi=10.1093/gbe/evy189}}</ref>

Endosymbiotic gene transfer is how we know about the [lost chloroplasts](/source/Chloroplast) in many [chromalveolate](/source/chromalveolate) 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](/source/diatoms) (a [heterokontophyte](/source/heterokontophyte)) now have a [red algal derived chloroplast](/source/red_algal_derived_chloroplast), the presence of many [green algal](/source/green_algal) genes in the diatom nucleus provide evidence that the diatom ancestor (probably the ancestor of all chromalveolates too) had a [green algal derived chloroplast](/source/green_algal_derived_chloroplast) at some point, which was subsequently replaced by the red chloroplast.<ref name="Science—Prasinophytes in chromalveolates">{{cite journal |vauthors=Moustafa A, Beszteri B, Maier UG, Bowler C, Valentin K, Bhattacharya D |title=Genomic footprints of a cryptic plastid endosymbiosis in diatoms |journal=Science |volume=324 |issue=5935 |pages=1724–6 |date=June 2009 |pmid=19556510 |doi=10.1126/science.1172983 |bibcode=2009Sci...324.1724M |s2cid=11408339 |url=https://epic.awi.de/id/eprint/20816/1/Mou2009a.pdf}}</ref>

In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast,<ref name=MolecularBiologyEvol-EndosymbioticGeneTransfer>{{cite journal |vauthors=Nowack EC, Vogel H, Groth M, Grossman AR, Melkonian M, Glöckner G |title=Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora |journal=Molecular Biology and Evolution |volume=28 |issue=1 |pages=407–22 |date=January 2011 |pmid=20702568 |doi=10.1093/molbev/msq209 |doi-access=free}}</ref> up to 18% in ''[Arabidopsis](/source/Arabidopsis)'', corresponding to about 4,500 protein-coding genes.<ref name="Current Biology—Algal genomics">{{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 |s2cid=17830745 |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=PNAS-RatesofctDNAevolution />

=== Proteins encoded by the chloroplast ===
Of the approximately three-thousand 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](/source/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](/source/gene_expression) in the nucleus, called ''[retrograde signaling](/source/retrograde_signaling_(cell_biology))''.<ref name=Science-ChloroplastSignals-NuclearGeneExpression>{{cite journal |vauthors=Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, Surpin M, Lim J, Mittler R, Chory J |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 |url=https://www.science.org/doi/10.1126/science.1140516 |bibcode=2007Sci...316..715K|url-access=subscription }}</ref>

===Protein synthesis===
{{See also|transcription (genetics)|Translation (biology)|label 1=Transcription|label 2=translation}}
Protein synthesis within chloroplasts relies on an [RNA polymerase](/source/RNA_polymerase) coded by the chloroplast's own genome, which is related to RNA polymerases found in bacteria. Chloroplasts also contain a mysterious second RNA polymerase that is encoded by the plant's nuclear genome. The two RNA polymerases may recognize and bind to different kinds of [promoters](/source/promoter_(genetics)) within the chloroplast genome.<ref name=Science-ChloroplastRNAPolymerases>{{cite journal |vauthors=Hedtke B, Börner T, Weihe A |title=Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis |journal=Science |volume=277 |issue=5327 |pages=809–11 |date=August 1997 |pmid=9242608 |doi=10.1126/science.277.5327.809}}</ref> The [ribosome](/source/ribosome)s in chloroplasts are similar to bacterial ribosomes.<ref name=ASM-ChloroplastRibosomesandProteinSynthesis1>{{cite journal |vauthors=Harris EH, Boynton JE, Gillham NW |title=Chloroplast ribosomes and protein synthesis |journal=Microbiological Reviews |volume=58 |issue=4 |pages=700–54 |date=December 1994 |pmid=7854253 |pmc=372988 |doi=10.1128/MMBR.58.4.700-754.1994}}</ref>

{{Expand section|Genome size differences between algae and land plants, chloroplast stuff coded by the nucleus, DNA replication, NADPH redox, special tRNA synthetases, etc.|date=January 2013}}

===RNA editing in plastids===
[RNA editing](/source/RNA_editing) is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior to translation to protein. The highly oxidative environment inside chloroplasts increases the rate of mutation so post-transcription repairs are needed to conserve functional sequences. The chloroplast editosome substitutes C -> U and U -> C at very specific locations on the transcript. This can change the codon for an amino acid or restore a non-functional pseudogene by adding an AUG start codon or removing a premature UAA stop codon.<ref name="Takenaka2013">{{cite journal |vauthors=Takenaka M, Zehrmann A, Verbitskiy D, Härtel B, Brennicke A |title=RNA editing in plants and its evolution |journal=Annual Review of Genetics |volume=47 |issue=1 |pages=335–52 |year=2013 |pmid=24274753 |doi=10.1146/annurev-genet-111212-133519}}</ref>

The editosome recognizes and binds to cis sequence upstream of the editing site. The distance between the binding site and editing site  varies by gene and proteins involved in the editosome.  Hundreds of different [PPR protein](/source/PPR_protein)s from the nuclear genome are involved in the RNA editing process. These proteins consist of 35-mer repeated amino acids, the sequence of which determines the cis binding site for the edited transcript.<ref name="Takenaka2013"/>

Basal land plants such as liverworts, mosses and ferns have hundreds of different editing sites while flowering plants typically have between thirty and forty. Parasitic plants such as [Epifagus virginiana](/source/Epifagus_virginiana) show a loss of RNA editing resulting in a loss of function for photosynthesis genes.<ref>{{cite journal |vauthors=Tillich M, Krause K |title=The ins and outs of editing and splicing of plastid RNAs: lessons from parasitic plants |journal=New Biotechnology |volume=27 |issue=3 |pages=256–66 |date=July 2010 |pmid=20206308 |doi=10.1016/j.nbt.2010.02.020 |series=Special Issue: Biotechnology Annual Review 2010RNA Basics and Biotechnology Applications}}</ref>

==DNA replication==

===Leading model of cpDNA replication===
thumb|upright=2.0|Chloroplast DNA replication via multiple D loop mechanisms. Adapted from Krishnan NM, Rao BJ's paper "A comparative approach to elucidate chloroplast genome replication."
The mechanism for chloroplast DNA (cpDNA) replication has not been conclusively determined, but two main models have been proposed. Scientists have attempted to observe chloroplast replication via [electron microscopy](/source/electron_microscopy) since the 1970s.<ref name=Krishnan>{{cite journal |vauthors=Krishnan NM, Rao BJ |title=A comparative approach to elucidate chloroplast genome replication |journal=BMC Genomics |volume=10 |issue=237 |page=237 |date=May 2009 |pmid=19457260 |pmc=2695485 |doi=10.1186/1471-2164-10-237 |doi-access=free}}</ref><ref name=Heinhorst>{{cite journal |last1=Heinhorst, Gordon C. Cannon |first1=Sabine |title=DNA replication in chloroplasts |journal=Journal of Cell Science |date=1993 |volume=104 |pages=1–9 |doi=10.1242/jcs.104.1.1 |url=https://aquila.usm.edu/cgi/viewcontent.cgi?article=7560&context=fac_pubs|url-access=subscription }}</ref> The results of the microscopy experiments led to the idea that chloroplast DNA replicates using a double displacement loop (D-loop). As the [D-loop](/source/D-loop) moves through the circular DNA, it adopts a theta intermediary form, also known as a Cairns replication intermediate, and completes replication with a rolling circle mechanism.<ref name="Krishnan"/><ref name="The Plant Cell—Linear chloroplast DNA"/> Replication starts at specific points of origin. Multiple [replication fork](/source/replication_fork)s open up, allowing replication machinery to replicate the DNA. As replication continues, the forks grow and eventually converge. The new cpDNA structures separate, creating daughter cpDNA chromosomes.

In addition to the early microscopy experiments, this model is also supported by the amounts of [deamination](/source/deamination) seen in cpDNA.<ref name="Krishnan"/> Deamination occurs when an [amino group](/source/amino_group) is lost and is a [mutation](/source/mutation) that often results in base changes. When adenine is deaminated, it becomes [hypoxanthine](/source/hypoxanthine) (H). Hypoxanthine can bind to [cytosine](/source/cytosine), and when the HC base pair is replicated, it becomes a GC (thus, an A → G base change).<ref name=Biocyclopedia>{{cite web |title=Effect of chemical mutagens on nucleotide sequence |url=http://www.biocyclopedia.com/index/genetics/mutations_molecular_level_mechanism/effect_of_chemical_mutagens_on_nucleotide_sequence.php |website=Biocyclopedia |access-date=24 October 2015}}</ref> 
thumb|left|400px|Over time, base changes in the DNA sequence can arise from deamination mutations. When adenine is deaminated, it becomes hypoxanthine, which can pair with cytosine. During replication, the cytosine will pair with guanine, causing an A → G base change.
In cpDNA, there are several A → G deamination gradients. DNA becomes susceptible to deamination events when it is single stranded. When replication forks form, the strand not being copied is single stranded, and thus at risk for A → G deamination. Therefore, gradients in deamination indicate that replication forks were most likely present and the direction that they initially opened (the highest gradient is most likely nearest the start site because it was single stranded for the longest amount of time).<ref name="Krishnan"/> This mechanism is still the leading theory today; however, a second theory suggests that most cpDNA is actually linear and replicates through homologous recombination. It further contends that only a minority of the genetic material is kept in circular chromosomes while the rest is in branched, linear, or other complex structures.<ref name="Krishnan"/><ref name="The Plant Cell—Linear chloroplast DNA"/>

===Alternative model of replication===
One of the main competing models for cpDNA asserts that most cpDNA is linear and participates in [homologous recombination](/source/homologous_recombination) and replication structures similar to [bacteriophage T4](/source/bacteriophage_T4).<ref name="The Plant Cell—Linear chloroplast DNA"/> It has been established that some plants have linear cpDNA, such as maize, and that more still contain complex structures that scientists do not yet understand;<ref name="The Plant Cell—Linear chloroplast DNA"/> however, the predominant view today is that most cpDNA is circular. When the original experiments on cpDNA were performed, scientists did notice linear structures; however, they attributed these linear forms to broken circles.<ref name="The Plant Cell—Linear chloroplast DNA"/> If the branched and complex structures seen in cpDNA experiments are real and not artifacts of concatenated circular DNA or broken circles, then a D-loop mechanism of replication is insufficient to explain how those structures would replicate.<ref name="The Plant Cell—Linear chloroplast DNA"/> At the same time, homologous recombination does not explain the multiple A → G gradients seen in plastomes.<ref name="Krishnan"/> This shortcoming is one of the biggest for the linear structure theory.

==Protein targeting and import==
{{See also|Protein targeting|label 1=Protein targeting}}

The movement of so many chloroplast genes to the nucleus means that many chloroplast [proteins](/source/proteins) that were supposed to be [translated](/source/Translation_(biology)) in the chloroplast are now synthesized in the cytoplasm. This means that these proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes.<ref name="Nature—Protein import">{{cite journal |vauthors=Soll J, Schleiff E |title=Protein import into chloroplasts |journal=Nature Reviews. Molecular Cell Biology |volume=5 |issue=3 |pages=198–208 |date=March 2004 |pmid=14991000 |doi=10.1038/nrm1333 |s2cid=32453554 |url=https://epub.ub.uni-muenchen.de/3587/1/3587.pdf}}</ref>

Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many became [exaptations](/source/exaptations), taking on new functions like participating in [cell division](/source/cell_division), [protein routing](/source/protein_routing), and even [disease resistance](/source/disease_resistance). A few chloroplast genes found new homes in the [mitochondrial genome](/source/mitochondrial_genome)—most became nonfunctional [pseudogenes](/source/pseudogenes), though a few [tRNA](/source/tRNA) genes still work in the [mitochondrion](/source/mitochondrion).<ref name="PNAS—Cyanobacterial genes in Arabidopsis" /> Some transferred chloroplast DNA protein products get directed to the [secretory pathway](/source/secretory_pathway)<ref name="PNAS—Cyanobacterial genes in Arabidopsis" /> (though many [secondary plastids](/source/secondary_plastids) are bounded by an outermost membrane derived from the host's [cell membrane](/source/cell_membrane), and therefore [topologically](/source/topologically) outside of the cell, because to reach the chloroplast from the [cytosol](/source/cytosol), you have to cross the [cell membrane](/source/cell_membrane), just like if you were headed for the [extracellular space](/source/extracellular_space). In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway).<ref name="RSTB—Endosymbiosis of plastids">{{cite journal |vauthors=Keeling PJ |title=The endosymbiotic origin, diversification and fate of plastids |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=365 |issue=1541 |pages=729–48 |date=March 2010 |pmid=20124341 |pmc=2817223 |doi=10.1098/rstb.2009.0103}}</ref>

Because the cell acquiring a chloroplast [already](/source/Chloroplast) had [mitochondria](/source/mitochondria) (and [peroxisomes](/source/peroxisomes), and a [cell membrane](/source/cell_membrane) for secretion), the new chloroplast host had to develop a unique [protein targeting system](/source/protein_targeting_system) to avoid having chloroplast proteins being sent to the wrong [organelle](/source/organelle).<ref name="Nature—Protein import" />

===Cytoplasmic translation and N-terminal transit sequences===
{{See also|Polypeptide|protein|translation (biology)|label 3=translation}}

{{plain image|File:Tetrapeptide structural formulae.svg|A [polypeptide](/source/polypeptide) with four [amino acids](/source/amino_acids) linked together. At the left is the [N-terminus](/source/N-terminus), with its [amino](/source/amino_group) (H<sub>2</sub>'''N''') group in green. The blue [C-terminus](/source/C-terminus), with its [carboxyl group](/source/carboxyl_group) ('''C'''O<sub>2</sub>H) is at the right.|350px|right|bottom|triangle|#00aa15}}

[Polypeptides](/source/Polypeptides), the precursors of [proteins](/source/proteins), are chains of [amino acids](/source/amino_acids). The two ends of a polypeptide are called the [N-terminus](/source/N-terminus), or ''amino end'', and the [C-terminus](/source/C-terminus), or ''carboxyl end''.<ref name="Biology 8th edition—Campbell & Reece—340">{{cite book |title=Biology 8th edition—Campbell & Reece |year=2008 |publisher=Benjamin Cummings |isbn=978-0-321-54325-7 |page=340}}</ref> For many (but not all)<ref name="Structure and Function of Plastids—Protein import">{{cite book |last1=Wise |first1=Robert R. |last2=Hoober |first2=J. Kenneth |name-list-style=vanc |title=Structure and function of plastids |year=2007 |publisher=Springer |location=Berlin |isbn=978-1-4020-6570-5 |pages=53–74 |url=https://books.google.com/books?id=FKeCVPbJ3asC&pg=PA59}}</ref> chloroplast proteins encoded by [nuclear](/source/cell_nucleus) genes, ''[cleavable transit peptides](/source/cleavable_transit_peptides)'' are added to the N-termini of the polypeptides, which are used to help direct the polypeptide to the chloroplast for import<ref name="Nature—Protein import" /><ref name="Plant Physiology—Motifs in Rubisco transit peptides">{{cite journal |vauthors=Lee DW, Lee S, Lee GJ, Lee KH, Kim S, Cheong GW, Hwang I |title=Functional characterization of sequence motifs in the transit peptide of Arabidopsis small subunit of rubisco |journal=Plant Physiology |volume=140 |issue=2 |pages=466–83 |date=February 2006 |pmid=16384899 |pmc=1361317 |doi=10.1104/pp.105.074575}}</ref> (N-terminal transit peptides are also used to direct polypeptides to plant [mitochondria](/source/mitochondria)).<ref name="The Plant Cell—14-3-3 proteins" />
N-terminal transit sequences are also called ''presequences''<ref name="Nature—Protein import" /> because they are located at the "front" end of a polypeptide—[ribosomes](/source/ribosomes) synthesize polypeptides from the N-terminus to the C-terminus.<ref name="Biology 8th edition—Campbell & Reece—340" />

Chloroplast transit peptides exhibit huge variation in length and [amino acid sequence](/source/amino_acid_sequence).<ref name="Plant Physiology—Motifs in Rubisco transit peptides" /> They can be from 20 to 150 amino acids long<ref name="Nature—Protein import" />—an unusually long length, suggesting that transit peptides are actually collections of [domains](/source/protein_domain) with different functions.<ref name="Plant Physiology—Motifs in Rubisco transit peptides" /> Transit peptides tend to be [positively charged](/source/positively_charged),<ref name="Nature—Protein import" /> rich in [hydroxylated](/source/hydroxyl_group) amino acids such as [serine](/source/serine), [threonine](/source/threonine), and [proline](/source/proline), and poor in [acidic](/source/acidic) amino acids like [aspartic acid](/source/aspartic_acid) and [glutamic acid](/source/glutamic_acid).<ref name="Plant Physiology—Motifs in Rubisco transit peptides" /> In an [aqueous solution](/source/aqueous_solution), the transit sequence forms a random coil.<ref name="Nature—Protein import" />

Not all chloroplast proteins include a N-terminal cleavable transit peptide though.<ref name="Nature—Protein import" /> Some include the transit sequence within the [functional part](/source/mature_protein) of the protein itself.<ref name="Nature—Protein import" /> A few have their transit sequence appended to their [C-terminus](/source/C-terminus) instead.<ref name="The Plant Cell—C-terminal transit sequences">{{cite journal |vauthors=Lung SC, Chuong SD |title=A transit peptide-like sorting signal at the C terminus directs the Bienertia sinuspersici preprotein receptor Toc159 to the chloroplast outer membrane |journal=The Plant Cell |volume=24 |issue=4 |pages=1560–78 |date=April 2012 |pmid=22517318 |pmc=3398564 |doi=10.1105/tpc.112.096248|bibcode=2012PlanC..24.1560L }}</ref> Most of the polypeptides that lack N-terminal targeting sequences are the ones that are sent to the [outer chloroplast membrane](/source/outer_chloroplast_membrane), plus at least one sent to the [inner chloroplast membrane](/source/inner_chloroplast_membrane).<ref name="Nature—Protein import" />

===Phosphorylation, chaperones, and transport===

After a chloroplast [polypeptide](/source/polypeptide) is synthesized on a [ribosome](/source/ribosome) in the [cytosol](/source/cytosol), [ATP](/source/Adenosine_triphosphate) energy can be used to [phosphorylate](/source/phosphorylate), or add a [phosphate group](/source/phosphate_group) to many (but not all) of them in their transit sequences.<ref name="Nature—Protein import" /> [Serine](/source/Serine) and [threonine](/source/threonine) (both very common in chloroplast transit sequences—making up 20–30% of the sequence)<ref name="JBC—Transit sequence phosphorylation" /> are often the [amino acids](/source/amino_acids) that accept the [phosphate group](/source/phosphate_group).<ref name="The Plant Cell—14-3-3 proteins">{{cite journal |vauthors=May T, Soll J |title=14-3-3 proteins form a guidance complex with chloroplast precursor proteins in plants |journal=The Plant Cell |volume=12 |issue=1 |pages=53–64 |date=January 2000 |pmid=10634907 |pmc=140214 |doi=10.1105/tpc.12.1.53|bibcode=2000PlanC..12...53M }}</ref><ref name="JBC—Transit sequence phosphorylation" /> The [enzyme](/source/protein_kinase) that carries out the phosphorylation is [specific](/source/enzyme_specificity) for chloroplast polypeptides, and ignores ones meant for [mitochondria](/source/mitochondria) or [peroxisomes](/source/peroxisomes).<ref name="JBC—Transit sequence phosphorylation">{{cite journal |vauthors=Waegemann K, Soll J |title=Phosphorylation of the transit sequence of chloroplast precursor proteins |journal=The Journal of Biological Chemistry |volume=271 |issue=11 |pages=6545–54 |date=March 1996 |pmid=8626459 |doi=10.1074/jbc.271.11.6545 |s2cid=26014578 |doi-access=free}}</ref>

Phosphorylation changes the polypeptide's shape,<ref name="JBC—Transit sequence phosphorylation" /> making it easier for [14-3-3 proteins](/source/14-3-3_proteins) to attach to the polypeptide.<ref name="Nature—Protein import" /><ref name="BBA—Tic-toc" /> In plants, [14-3-3 proteins](/source/14-3-3_proteins) only bind to chloroplast preproteins.<ref name="The Plant Cell—14-3-3 proteins" /> It is also bound by the ['''h'''eat '''s'''hock '''p'''rotein](/source/heat_shock_protein) [Hsp70](/source/Hsp70) that keeps the polypeptide from [folding](/source/protein_folding) prematurely.<ref name="Nature—Protein import" /> This is important because it prevents chloroplast proteins from assuming their active form and carrying out their chloroplast functions in the wrong place—the [cytosol](/source/cytosol).<ref name="The Plant Cell—14-3-3 proteins" /><ref name="BBA—Tic-toc">{{cite journal |vauthors=Jarvis P, Soll J |title=Toc, Tic, and chloroplast protein import |journal=Biochimica et Biophysica Acta (BBA) - Molecular Cell Research |volume=1541 |issue=1–2 |pages=64–79 |date=December 2001 |pmid=11750663 |doi=10.1016/S0167-4889(01)00147-1|hdl=2381/14128 |hdl-access=free }}</ref> At the same time, they have to keep just enough shape so that they can be recognized and imported into the chloroplast.<ref name="The Plant Cell—14-3-3 proteins" />

The heat shock protein and the 14-3-3 proteins together form a cytosolic guidance complex that makes it easier for the chloroplast polypeptide to get imported into the chloroplast.<ref name="Nature—Protein import" />

Alternatively, if a chloroplast preprotein's transit peptide is not phosphorylated, a chloroplast preprotein can still attach to a heat shock protein or [Toc159](/source/Toc159). These complexes can bind to the [TOC complex](/source/TOC_complex) on the outer chloroplast membrane using [GTP](/source/Guanosine_triphosphate) energy.<ref name="Nature—Protein import" />

===The translocon on the outer chloroplast membrane <span style="font-weight: 400; ">(TOC)</span>===

The [TOC complex](/source/TOC_complex), or ''['''t'''ranslocon](/source/translocon) on the '''o'''uter '''c'''hloroplast membrane'', is a collection of proteins that imports preproteins across the [outer chloroplast envelope](/source/outer_chloroplast_envelope). Five [subunits](/source/protein_subunit) of the TOC complex have been identified—two [GTP](/source/Guanosine_triphosphate)-binding proteins [Toc34](/source/Toc34) and [Toc159](/source/Toc159), the protein import tunnel [Toc75](/source/Toc75), plus the proteins [Toc64](/source/Toc64)<ref name="Nature—Protein import" /> and [Toc12](/source/Toc12).<ref name="Structure and Function of Plastids—Protein import" />

The first three proteins form a core complex that consists of one Toc159, four to five Toc34s, and four Toc75s that form four holes in a disk 13 [nanometers](/source/nanometers) across. The whole core complex weighs about 500 [kilodaltons](/source/kilodaltons). The other two proteins, Toc64 and Toc12, are associated with the core complex but are not part of it.<ref name="Structure and Function of Plastids—Protein import" />

====Toc34 and 33====

{{plain image|File:TOC34.png|Toc34 from a [pea plant](/source/pea_plant). Toc34 has three almost identical molecules (shown in slightly different shades of green), each of which forms a [dimer](/source/Protein_dimer) with one of its adjacent molecules. Part of a [GDP](/source/Guanosine_diphosphate) molecule binding site is highlighted in pink.<ref name="Nature—Toc34">{{cite journal |vauthors=Sun YJ, Forouhar F, Li Hm HM, Tu SL, Yeh YH, Kao S, Shr HL, Chou CC, Chen C, Hsiao CD |title=Crystal structure of pea Toc34, a novel GTPase of the chloroplast protein translocon |journal=Nature Structural Biology |volume=9 |issue=2 |pages=95–100 |date=February 2002 |pmid=11753431 |doi=10.1038/nsb744 |s2cid=21855733}}</ref>|350px|right|bottom|triangle|#58e11c}}

[Toc34](/source/Toc34) is an [integral protein](/source/integral_protein) in the outer chloroplast membrane that's anchored into it by its [hydrophobic](/source/hydrophobic)<ref name="Plant Physiology—Toc 159 A domain" /> [C-terminal](/source/C-terminal) tail.<ref name="Nature—Protein import" /><ref name="BBA—Tic-toc" /> Most of the protein, however, including its large [guanosine triphosphate](/source/guanosine_triphosphate) (GTP)-binding [domain](/source/protein_domain) projects out into the stroma.<ref name="BBA—Tic-toc" />

Toc34's job is to catch some chloroplast [preproteins](/source/preproteins) in the [cytosol](/source/cytosol) and hand them off to the rest of the TOC complex.<ref name="Nature—Protein import" /> When [GTP](/source/Guanosine_triphosphate), an energy molecule similar to [ATP](/source/Adenosine_triphosphate) attaches to Toc34, the protein becomes much more able to bind to many chloroplast preproteins in the [cytosol](/source/cytosol).<ref name="Nature—Protein import" /> The chloroplast preprotein's presence causes Toc34 to break GTP into [guanosine diphosphate](/source/guanosine_diphosphate) (GDP) and [inorganic phosphate](/source/inorganic_phosphate). This loss of GTP makes the Toc34 protein release the chloroplast preprotein, handing it off to the next TOC protein.<ref name="Nature—Protein import" /> Toc34 then releases the depleted GDP molecule, probably with the help of an unknown [GDP exchange factor](/source/GDP_exchange_factor). A [domain](/source/protein_domain) of [Toc159](/source/Toc159) might be the exchange factor that carry out the GDP removal. The Toc34 protein can then take up another molecule of GTP and begin the cycle again.<ref name="Nature—Protein import" />

Toc34 can be turned off through [phosphorylation](/source/phosphorylation). A [protein kinase](/source/protein_kinase) drifting around on the outer chloroplast membrane can use [ATP](/source/Adenosine_triphosphate) to add a [phosphate group](/source/phosphate_group) to the Toc34 protein, preventing it from being able to receive another [GTP](/source/Guanosine_triphosphate) molecule, inhibiting the protein's activity. This might provide a way to regulate protein import into chloroplasts.<ref name="Nature—Protein import" /><ref name="BBA—Tic-toc" />

''[Arabidopsis thaliana](/source/Arabidopsis_thaliana)'' has two [homologous](/source/Homologous_series) proteins, [AtToc33](/source/AtToc33) and [AtToc34](/source/AtToc34) (The ''At'' stands for '''''A'''rabidopsis '''t'''haliana''),<ref name="Nature—Protein import" /><ref name="BBA—Tic-toc" /> which are each about 60% identical in [amino acid sequence](/source/amino_acid_sequence) to Toc34 in [peas](/source/peas) (called ''ps''Toc34).<ref name="BBA—Tic-toc" /> AtToc33 is the most common in ''Arabidopsis'',<ref name="BBA—Tic-toc" /> and it is the functional [analogue](/source/analogy_(biology)) of Toc34 because it can be turned off by phosphorylation. AtToc34 on the other hand cannot be phosphorylated.<ref name="Nature—Protein import" /><ref name="BBA—Tic-toc" />

====Toc159====

[Toc159](/source/Toc159) is another [GTP](/source/Guanosine_triphosphate) binding TOC [subunit](/source/protein_subunit), like [Toc34](/source/Toc34). Toc159 has three [domains](/source/protein_domain). At the [N-terminal](/source/N-terminal) end is the A-domain, which is rich in [acidic amino acids](/source/acidic_amino_acids) and takes up about half the protein length.<ref name="Nature—Protein import" /><ref name="Plant Physiology—Toc 159 A domain">{{cite journal |vauthors=Agne B, Andrès C, Montandon C, Christ B, Ertan A, Jung F, Infanger S, Bischof S, Baginsky S, Kessler F |title=The acidic A-domain of Arabidopsis TOC159 occurs as a hyperphosphorylated protein |journal=Plant Physiology |volume=153 |issue=3 |pages=1016–30 |date=July 2010 |pmid=20457805 |pmc=2899928 |doi=10.1104/pp.110.158048}}</ref> The A-domain is often [cleaved](/source/protein_cleavage) off, leaving an 86 [kilodalton](/source/kilodalton) fragment called [Toc86](/source/Toc86).<ref name="Plant Physiology—Toc 159 A domain" /> In the middle is its [GTP](/source/Guanosine_triphosphate) binding domain, which is very similar to the [homologous](/source/homology_(biology)) GTP-binding domain in Toc34.<ref name="Nature—Protein import" /><ref name="Plant Physiology—Toc 159 A domain" /> At the [C-terminal](/source/C-terminal) end is the [hydrophilic](/source/hydrophilic) M-domain,<ref name="Nature—Protein import" /> which anchors the protein to the outer chloroplast membrane.<ref name="Plant Physiology—Toc 159 A domain" />

Toc159 probably works a lot like Toc34, recognizing proteins in the cytosol using [GTP](/source/Guanosine_triphosphate). It can be regulated through [phosphorylation](/source/phosphorylation), but by a different [protein kinase](/source/protein_kinase) than the one that phosphorylates Toc34.<ref name="Structure and Function of Plastids—Protein import" /> Its M-domain forms part of the tunnel that chloroplast preproteins travel through, and seems to provide the force that pushes preproteins through, using the energy from [GTP](/source/Guanosine_triphosphate).<ref name="Nature—Protein import" />

Toc159 is not always found as part of the TOC complex—it has also been found dissolved in the [cytosol](/source/cytosol). This suggests that it might act as a shuttle that finds chloroplast preproteins in the cytosol and carries them back to the TOC complex. There isn't a lot of direct evidence for this behavior though.<ref name="Nature—Protein import" />

A family of Toc159 proteins, [Toc159](/source/Toc159), [Toc132](/source/Toc132), [Toc120](/source/Toc120), and [Toc90](/source/Toc90) have been found in ''[Arabidopsis thaliana](/source/Arabidopsis_thaliana)''. They vary in the length of their A-domains, which is completely gone in Toc90. Toc132, Toc120, and Toc90 seem to have specialized functions in importing stuff like nonphotosynthetic preproteins, and can't replace Toc159.<ref name="Nature—Protein import" />

====Toc75====

{{plain image|File:Sucrose porin 1a0s.png|'''β-barrel''' The general shape of a β-barrel is a hollow cylinder lined by multiple [β-sheets](/source/%CE%B2-sheets). Note that the protein depicted is ''not'' Toc75 specifically.|300px|right|top|triangle|#dfc400}}

[Toc75](/source/Toc75) is the most abundant protein on the outer chloroplast envelope. It is a [transmembrane](/source/transmembrane) tube that forms most of the TOC pore itself. Toc75 is a [β-barrel](/source/%CE%B2-barrel) channel lined by 16 [β-pleated sheets](/source/%CE%B2-pleated_sheets).<ref name="Nature—Protein import" /> The hole it forms is about 2.5 [nanometers](/source/nanometers) wide at the ends, and shrinks to about 1.4–1.6 nanometers in diameter at its narrowest point—wide enough to allow partially folded chloroplast preproteins to pass through.<ref name="Nature—Protein import" />

Toc75 can also bind to chloroplast preproteins, but is a lot worse at this than Toc34 or Toc159.<ref name="Nature—Protein import" />

''[Arabidopsis thaliana](/source/Arabidopsis_thaliana)'' has multiple [isoforms](/source/isoforms) of [Toc75](/source/Toc75) that are named by the [chromosomal](/source/chromosomal) positions of the [genes](/source/genes) that code for them. [AtToc75 III](/source/AtToc75_III) is the most abundant of these.<ref name="Nature—Protein import" />

===The translocon on the inner chloroplast membrane <span style="font-weight: 400; ">(TIC)</span>===

The [TIC translocon](/source/TIC_translocon), or '''''t'''ranslocon on the '''i'''nner '''c'''hloroplast membrane [translocon](/source/translocon)''<!--Yes, that's what the source says--><ref name="Nature—Protein import" /> is another protein complex that imports proteins across the [inner chloroplast envelope](/source/inner_chloroplast_envelope). Chloroplast polypeptide chains probably often travel through the two complexes at the same time, but the TIC complex can also retrieve preproteins lost in the [intermembrane space](/source/chloroplast_intermembrane_space).<ref name="Nature—Protein import" />

Like the [TOC translocon](/source/Toc_translocon), the TIC translocon has a large core [complex](/source/Protein_complex) surrounded by some loosely associated peripheral proteins like [Tic110](/source/Tic110), [Tic40](/source/Tic40), and [Tic21](/source/Tic21).<ref name="Science—TIC">{{cite journal |vauthors=Kikuchi S, Bédard J, Hirano M, Hirabayashi Y, Oishi M, Imai M, Takase M, Ide T, Nakai M |title=Uncovering the protein translocon at the chloroplast inner envelope membrane |journal=Science |volume=339 |issue=6119 |pages=571–4 |date=February 2013 |pmid=23372012 |doi=10.1126/science.1229262 |bibcode=2013Sci...339..571K |s2cid=5062593}}</ref>
The core complex weighs about one million [dalton](/source/dalton_(unit))s and contains [Tic214](/source/Tic214), [Tic100](/source/Tic100), [Tic56](/source/Tic56), and [Tic20 I](/source/Tic20_I), possibly three of each.<ref name="Science—TIC" />

====Tic20====

[Tic20](/source/Tic20) is an [integral](/source/Integral_membrane_protein) protein thought to have four [transmembrane](/source/Transmembrane_domain) [α-helices](/source/%CE%B1-helices).<ref name="Nature—Protein import" /> It is found in the 1 million [dalton](/source/Dalton_(unit)) TIC complex.<ref name="Science—TIC" /> Because it is similar to [bacterial](/source/Bacterial_protein) [amino acid](/source/amino_acid) transporters and the [mitochondrial](/source/mitochondrial) import protein [Tim17](/source/Tim17)<ref name="Nature—Protein import" /> (''['''t'''ranslocase](/source/Translocase_of_the_inner_membrane) on the ['''i'''nner '''m'''itochondrial '''m'''embrane](/source/Inner_mitochondrial_membrane)''),<ref>{{Cite book |isbn=978-3-540-21489-2 |title=Mitochondrial Function and Biogenesis |url=https://books.google.com/books?id=ie5ZmOYHpVEC&pg=PA59 |publisher=Springer |page=59 |year=2004 |first1=Sean P |last1=Curran |first2=Carla M |last2=Koehler |name-list-style=vanc}}</ref> it has been proposed to be part of the TIC import channel.<ref name="Nature—Protein import" /> There is no ''[in vitro](/source/in_vitro)'' evidence for this though.<ref name="Nature—Protein import" /> In ''[Arabidopsis thaliana](/source/Arabidopsis_thaliana)'', it is known that for about every five [Toc75](/source/Toc75) proteins in the outer chloroplast membrane, there are two [Tic20 I](/source/Tic20_I) proteins (the main [form](/source/Isoform) of Tic20 in [''Arabidopsis''](/source/Arabidopsis_thaliana)) in the inner chloroplast membrane.<ref name="Science—TIC" />

Unlike [Tic214](/source/Tic214), [Tic100](/source/Tic100), or [Tic56](/source/Tic56), Tic20 has [homologous](/source/homology_(biology)) relatives in [cyanobacteria](/source/cyanobacteria) and nearly all chloroplast lineages, suggesting it evolved before the first chloroplast endosymbiosis. [Tic214](/source/Tic214), [Tic100](/source/Tic100), and [Tic56](/source/Tic56) are unique to [chloroplastidan](/source/chloroplastidan) chloroplasts, suggesting that they evolved later.<ref name="Science—TIC" />

====Tic214====
[Tic214](/source/Tic214) is another TIC core complex protein, named because it weighs just under 214 [kilodaltons](/source/kilodaltons). It is 1786 [amino acids](/source/amino_acids) long and is thought to have six [transmembrane domains](/source/transmembrane_domains) on its [N-terminal](/source/N-terminal) end. Tic214 is notable for being coded for by chloroplast DNA, more specifically the first [open reading frame](/source/open_reading_frame) ''[ycf1](/source/ycf1)''. Tic214 and [Tic20](/source/Tic20) together probably make up the part of the one million [dalton](/source/Dalton_(unit)) TIC complex that spans the [entire membrane](/source/Transmembrane_protein). Tic20 is buried inside the complex while Tic214 is exposed on both sides of the [inner chloroplast membrane](/source/inner_chloroplast_membrane).<ref name="Science—TIC" />

====Tic100====
[Tic100](/source/Tic100) is a [nuclear encoded](/source/nuclear_genome) protein that's 871 [amino acids](/source/amino_acids) long. The 871 amino acids collectively weigh slightly less than 100 thousand [daltons](/source/dalton_(unit)), and since the mature protein probably doesn't lose any amino acids when itself imported into the chloroplast (it has no [cleavable transit peptide](/source/cleavable_transit_peptide)), it was named Tic100. Tic100 is found at the edges of the 1 million dalton complex on the side that faces the [chloroplast intermembrane space](/source/chloroplast_intermembrane_space).<ref name="Science—TIC" />

====Tic56====
[Tic56](/source/Tic56) is also a [nuclear encoded](/source/nuclear_genome) protein. The [preprotein](/source/preprotein) its gene encodes is 527 amino acids long, weighing close to 62 thousand [daltons](/source/dalton_(unit)); the mature form probably undergoes processing that trims it down to something that weighs 56 thousand daltons when it gets imported into the chloroplast. Tic56 is largely embedded inside the 1 million dalton complex.<ref name="Science—TIC" />

Tic56 and [Tic100](/source/Tic100) are highly [conserved](/source/gene_conservation) among land plants, but they don't resemble any protein whose function is known. Neither has any [transmembrane domains](/source/transmembrane_domains).<ref name="Science—TIC" />
{{Clear}}
<!--
<div style="float: right; clear: right; width: 30%; background: #73d9ff; height: 30px; text-align: center; line-height: 30px; color: white;">'''Epiplastid membrane'''</div>

<div style="float: right; clear: right; margin-top: 100px; width: 20%; background: #0dc0b2; height: 30px; text-align: center; line-height: 30px; color: white;">'''Periplastid membrane'''</div>

<div style="float: right; clear: right; margin-top: 100px; width: 40%; background: #0dc04f; height: 30px; text-align: center; line-height: 30px; color: white;">'''Outer chloroplast membrane'''</div>

<div style="float: right; clear: right; margin-top: 100px; width: 40%; background: #0dc04f; height: 30px; text-align: center; line-height: 30px; color: white;">'''Inner chloroplast membrane'''</div>

-->

== See also ==
* [List of sequenced plastomes](/source/List_of_sequenced_plastomes)
* [Mitochondrial DNA](/source/Mitochondrial_DNA)

== References ==

{{Reflist|refs=
<ref name=" Stocking1959">{{cite journal |author1=Stocking, C. R. |author2=Gifford, E. M. |name-list-style=amp |title=Incorporation of thymidine into chloroplasts of Spirogyra |journal=Biochemical and Biophysical Research Communications |year=1959 |volume=1 |issue=3 |pages=159–164 |doi=10.1016/0006-291X(59)90010-5|bibcode=1959BBRC....1..159S }}</ref>
<ref name=" Ris1962">{{cite journal |author1=Ris, H. |author2=Plaut, W. |name-list-style=amp |title=Ultrastructure of DNA-containing areas in the chloroplast of Chlamydomonas |journal=J. Cell Biol. |year=1962 |volume=13 |issue=3 |pages=383–91 |doi=10.1083/jcb.13.3.383 |pmid=14492436 |pmc=2106071}}</ref>
<ref name=" Heber1962">{{cite journal |author1=Heber, U. |title=Protein synthesis in chloroplasts during photosynthesis |journal=Nature |year=1962 |volume=195 |issue=1 |pages=91–92 |doi=10.1038/195091a0 |pmid=13905812 |bibcode=1962Natur.195...91H |s2cid=4265095}}</ref>
<ref name=" Lyttleton1962">{{cite journal |author1=Lyttleton, J. W. |title=Isolation of ribosomes from spinach chloroplasts |journal=Exp. Cell Res. |year=1962 |volume=26 |issue=1 |pages=312–317 |doi=10.1016/0014-4827(62)90183-0 |pmid=14467684}}</ref>
<ref name=BioscienceExplained>{{cite book |last=Dann |first=Leighton |name-list-style=vanc |title=Bioscience—Explained |year=2002 |publisher=BIOSCIENCE EXPLAINED |location=Green DNA |url=http://www.bioscience-explained.org/ENvol1_2/pdf/ctDNAEN.pdf}}</ref>
<ref name=Springer-TheChloroplast-18>{{cite book |last=Sandelius |first=Anna Stina |name-list-style=vanc |title=The Chloroplast: Interactions with the Environment |year=2009 |publisher=Springer |isbn=978-3-540-68696-5 |page=18 |url=https://books.google.com/books?id=aQR__H2XBnUC&pg=PA18}}</ref>
<ref name=" NCBI-Organelle">{{cite web |url=https://www.ncbi.nlm.nih.gov/datasets/organelle/?taxon=2759 |title=NCBI Organelle Genome Resources |publisher=National Institute of Health |access-date=August 18, 2021}}</ref>
<ref name="Ohyama1986">{{cite journal |author1=Shinozaki, K. |author2=Ohme, M. |author3=Tanaka, M. |author4=Wakasugi, T. |author5=Hayashida, N. |author6=Matsubayashi, T. |author7=Zaita, N. |author8=Chunwongse, J. |author9=Obokata, J. | author10= Yamaguchi-Shinozaki, K. |name-list-style=amp |title=The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression |journal=EMBO J. |year=1986 |volume=5 |issue=9 |pages=2043–2049 |doi=10.1002/j.1460-2075.1986.tb04464.x |pmid=16453699 |pmc=1167080}}</ref>
<ref name="Shinozaki1986">{{cite journal |author1=Ohyama, K. |author2=Fukuzawa, H. |author3=Kohchi, T. |author4=Shirai, H. |author5=Sano, T. |author6=Sano, S. |author7=Umesono, K. |author8=Shiki, Y. |author9=Takeuchi, M. | author10= Chang, Z. |author11=Aota, S. |name-list-style=amp |title=Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA |journal=Nature |year=1986 |volume=322 |issue=6079 |pages=572–574 |doi=10.1038/322572a0 |bibcode=1986Natur.322..572O |s2cid=4311952}}</ref>
<ref name="Kaneko1997">{{cite journal |author1=Kaneko, T. |author2=Tabata, S. |name-list-style=amp |title=Complete genome structure of the unicellular cyanobacterium Synechocystis sp. PCC6803 |journal=Plant Cell Physiol. |year=1997 |volume=38 |issue=11 |pages=1171–1176 |doi=10.1093/oxfordjournals.pcp.a029103 |pmid=9435137 |doi-access=free}}</ref>
<ref name="Sato1999">{{cite journal |author1=Sato, S. |author2=Nakamura, Y. |author3=Kaneko, T. |author4=Asamizu, E. |author5=Tabata, S. |name-list-style=amp |title=Complete structure of the chloroplast genome of Arabidopsis thaliana |journal=DNA Res. |year=1999 |volume=6 |issue=5 |pages=283–290 |doi=10.1093/dnares/6.5.283 |pmid=10574454 |doi-access=free}}</ref>
<ref name="Daniell2016">{{cite journal |author1=Daniell, H. |author2=Lin, C. |author3=Yu, M. |author4=Chang, W |name-list-style=amp |title=Chloroplast genomes: diversity, evolution, and applications in genetic engineering |journal=Genome Biol. |year=2016 |volume=17 |issue=1 |page=134 |doi=10.1186/s13059-016-1004-2 |pmid=27339192 |pmc=4918201 |doi-access=free}}</ref>
<ref name="Clegg1994">{{cite journal |author1=Clegg, M. T. |author2=Gaut, B. S. |author3=Learn, G. H. |author4=Morton, B. R. |name-list-style=amp |title=Rates and patterns of chloroplast DNA evolution |journal=PNAS |year=1994 |volume=91 |issue=15 |pages=6795–6801 |doi=10.1073/pnas.91.15.6795 |pmid=8041699 |pmc=44285 |bibcode=1994PNAS...91.6795C |doi-access=free}}</ref>
<ref name="Berry2013">{{cite journal |author1=Berry, J. O. |author2=Yerramsetty, P. |author3=Zielinski, A. M. |author4=Mure, C. M. |name-list-style=amp |title=Photosynthetic gene expression in higher plants |journal=Photosynth. Res. |year=2013 |volume=117 |issue=1 |pages=91–120 |doi=10.1007/s11120-013-9880-8 |pmid=23839301 |bibcode=2013PhoRe.117...91B |s2cid=16536768}}</ref>
<ref name=PNAS-RatesofctDNAevolution>{{cite journal |vauthors=Clegg MT, Gaut BS, Learn GH, Morton BR |title=Rates and patterns of chloroplast DNA evolution |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=91 |issue=15 |pages=6795–801 |date=July 1994 |pmid=8041699 |pmc=44285 |doi=10.1073/pnas.91.15.6795 |bibcode=1994PNAS...91.6795C |doi-access=free}}</ref>

}}

{{Authority control}}

Category:Cell anatomy
Category:Chromosomes
Category:DNA
Category:Plant genes
Category:Photosynthesis

---
Adapted from the Wikipedia article [Plastid DNA](https://en.wikipedia.org/wiki/Plastid_DNA) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Plastid_DNA?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.