Structure of a typical higher-plant chloroplast
Chloroplasts // are organelles found in plant cells and some other eukaryotic organisms. As well as conducting photosynthesis, they carry out almost all fatty acid synthesis in plants, and are involved in a plant's immune response. A chloroplast is a type of plastid which specializes in photosynthesis. During photosynthesis, chloroplasts capture the sun's light energy, and store it in the energy storage molecules ATP and NADPH while freeing oxygen from water. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle.1
The word chloroplast (χλωροπλάστης) is derived from the Greek words chloros (χλωρός), which means green, and plastes (πλάστης), which means "the one who forms".2
Chloroplasts are one of the many different types of organelles in the plant cell. However, unlike most cellular organelles, they are considered to have originated from cyanobacteria through endosymbiosis—when a eukaryotic cell engulfed a photosynthesizing cyanobacterium which remained and became a permanent resident in the cell. Mitochondria are thought to have come from a similar event, where a ærobic prokaryote was engulfed.3 This origin of chloroplasts was first suggested by Konstantin Mereschkowski in 19054 after Andreas Schimper observed that chloroplasts closely resemble cyanobacteria in 1883.5
Cyanobacteria are considered the ancestors of chloroplasts. They are sometimes called blue-green algae even though they are prokaryotes. They are a diverse phylum of bacteria capable of carrying out photosynthesis, and are gram-negative, meaning they have two cell membranes. They also contain a thick peptidoglycan cell wall which is located between their two cell membranes.6 Like chloroplasts, they have thylakoids inside of them.7 On the thylakoid membranes are photosynthetic pigments, including chlorophyll a.8 Phycobilins are also common cyanobacterial pigments, usually organized into hemispherical phycobilisomes attached to the outside of the thylakoid membranes. (Phycobilins are not shared with all chloroplasts though).98
A eukaryote with mitochondria engulfed a cyanobacterium in an event of serial primary endosymbiosis, creating a lineage of cells with both organelles.3 It is important to note that the cyanobacterial endosymbiont already had a double membrane—the phagosomal vacuole-derived membrane was lost.10
Somewhere around a billion years ago,11 a free-living cyanobacterium entered an early eukaryotic cell, either as food or an internal parasite,3 and managed to escape the phagocytic vacuole it was contained in.8 The two innermost lipid-bilayer membranes that surround all chloroplasts12 correspond to the outer and inner membranes of the ancestral cyanobacterium's gram negative cell wall,131410 and not the phagosomal membrane from the host, which was probably lost.10 The new cellular resident quickly became an advantage, providing food for the eukaryotic host, which allowed it to live within it.3 Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to the nucleus of the host.15 Some of its proteins were then synthesized in the cytoplasm of the host cell, and imported back into the chloroplast.1516
Chloroplasts are believed to have arisen after mitochondria, since all eukaryotes contain mitochondria, but not all have chloroplasts.317 This is called serial endosymbiosis—an early eukaryote engulfing the mitochondrion ancestor, and some descendants of it then engulfing the chloroplast ancestor, creating a cell with both chloroplasts and mitochondria.3
Whether or not chloroplasts came from a single endosymbiotic event, or many independent engulfments across various eukaryotic lineages has been long debated, but it is now generally held that all organisms with chloroplasts either share a single ancestor or obtained their chloroplast from organisms that share a common ancestor that took in a cyanobacterium 600–1600 million years ago.11
These chloroplasts, which can be traced back directly to a cyanobacterial ancestor are known as primary plastids18 ("plastid" in this context means the almost the same thing as chloroplast3). All primary chloroplasts belong to one of three chloroplast lineages—the glaucophyte chloroplast lineage, the rhodophyte, or red algal chloroplast lineage, or the chloroplastidan, or green chloroplast lineage.19 The second two are the largest,10 and the green chloroplast lineage is the one that contains the land plants.10
A primary endosymbiosis
event gave rise to three main
lineages of chloroplasts in
the glaucophytes, chlorophyta,
Some of these algae were
subsequently engulfed by
other algae, becoming
secondary (or tertiary)
a The apicomplexans (malaria
parasites), contain a red algal
endosymbiont with a non-
b 2–3 chloroplast membranes8
a c 2–4 chloroplast membranes8
|Green algal dinophytes|
||Peridinin-type dinophytes b|
|Haptophyta||Haptophyte dinophytes c|
|Primary endosymbiosis||Secondary endosymbiosis||Tertiary endosymbiosis|
The alga Cyanophora, a glaucophyte, is thought to be one of the first organisms to contain a chloroplast.16 The glaucophyte chloroplast group is the smallest of the three primary chloroplast lineages, being found in only thirteen species,10 and is thought to be the one that branched off the earliest.111021 Glaucophytes have chloroplasts which retain a peptidoglycan wall between their double membranes,18 like their cyanobacterial parent.6 For this reason, glaucophyte chloroplasts are also known as muroplasts.18 Glaucophyte chloroplasts also contain concentric unstacked thylakoids which surround a carboxysome, an icosahedral structure that glaucophyte chloroplasts and cyanobacteria keep their carbon fixation enzyme rubisco in. The starch they synthesize collects outside the chloroplast.8 Like cyanobacteria, glaucophyte chloroplast thylakoids are studded with light collecting structures called phycobilisomes.818 For these reasons, glaucophyte chloroplasts are considered a primitive intermediate between cyanobacteria and the more evolved chloroplasts in red algae and plants.18
Diversity of red algae Clockwise from top left: Bornetia secundiflora, Peyssonnelia squamaria, Cyanidium, Laurencia, Callophyllis laciniata. Many red algae are commonly called "seaweeds" due to their multicellularity and size.22 Red algal chloroplasts are characterized by phycobilin pigments which often give them their reddish color.22
Rhodoplasts have a double membrane with an intermembrane space and phycobilin pigments organized into phycobilisomes on the thylakoid membranes, preventing their thylakoids from stacking.8 Some contain pyrenoids.18 Rhodoplasts have chlorophyll a and phycobilins21 for photosynthetic pigments; the phycobilin phycoerytherin is responsible for giving many red algae their distinctive red color.22 However, since they also contain the blue-green chlorophyll a and other pigments, many are reddish to purple from the combination.18 The red phycoerytherin pigment is an adaptation to help red algae catch more sunlight in deep water18—as such, some red algae that live in shallow water have less phycoerytherin in their rhodoplasts, and can appear more greenish.22 Rhodoplasts synthesize a form of starch called floridean,18 which collects into granules outside the rhodoplast, in the cytoplasm of the red alga.8
The chloroplastidan chloroplasts, or green chloroplasts, are another large, highly diverse primary chloroplast lineage. They are commonly known as the green algae and land plants.24 They differ from glaucophyte and red algal chloroplasts in that they have lost their phycobilisomes, and contain chlorophyll b instead.8 Most green chloroplasts are (obviously) green, though some, like some forms of Hæmatococcus pluvialis aren't, due to accessory pigments that override the chlorophylls' green colors. Chloroplastidan chloroplasts have lost the peptidoglycan wall between their double membrane, and have replaced it with an intermembrane space.8 Some plants seem to have kept the genes for the synthesis of the peptidoglycan layer, though they've been repurposed for use in chloroplast division instead.25
Most of the chloroplasts depicted in this article are green chloroplasts.
Green algae and plants keep their starch inside their chloroplasts,82124 and in plants and some algae, the chloroplast thylakoids are arranged in grana stacks. Some green algal chloroplasts contain a structure called a pyrenoid,8 which is functionally similar to the glaucophyte carboxysome in that it's where rubisco and CO2 are concentrated in the chloroplast.26
The helicosproidia are nonphotosynthetic parasitic green algae that are thought to contain a vestigal chloroplast.21 Genes from a chloroplast27 and nuclear genes indicating the presence of a chloroplast have been found in helicosporoidia.21 even if nobody's seen the chloroplast itself.21
Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga that contained a chloroplast. These chloroplasts are known as secondary plastids.18
While primary chloroplasts have a double membrane from their cyanobacterial ancestor, secondary chloroplasts have additional membranes outside of the original two, as a result of the secondary endosymbiotic event, when a nonphotosynthetic eukaryote engulfed an chloroplast-containing alga but failed to digest it—much like the cyanobacterium at the beginning of this story.10 The engulfed alga was broken down, leaving only its chloroplast, and sometimes its cell membrane and nucleus, forming a chloroplast with three to four membranes28—the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and the phagosomal vacuole from the host's cell membrane.10
Diagram of a four membraned chloroplast containing a nucleomorph.
The genes in the phagocytosed eukaryote's nucleus are often transferred to the secondary host's nucleus.10 Cryptomonads and chlorarachniophytes retain the phagocytosed eukaryote's nucleus, an object called a nucleomorph,10 located between the second and third membranes of the chloroplast.816
All secondary chloroplasts come from 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.10
Green algae have been taken up by the euglenids, chlorarachniophytes, a lineage of dinoflagellates,21 and possibly the ancestor of the chromalveolates29 in three or four separate engulfments.30 Many green algal derived chloroplasts contain pyrenoids, but unlike chloroplasts in their green algal ancestors, starch collects in granules outside the chloroplast.8
Euglenophytes are a group of common flagellated protists that contain chloroplasts derived from a green alga.10 Euglenophyte chloroplasts have three membranes—it's thought that the membrane of the primary endosymbiont was lost, leaving the cyanobacterial membranes, and the secondary host's phagosomal membrane.10 Euglenophyte chloroplasts have a pyrenoid and thylakoids stacked in groups of three. Starch is stored in the form of paramylon, which is contained in membrane-bound granules in the cytoplasm of the euglenophyte.821
Chlorarachniophytes (//) are a rare group of organisms that also contain chloroplasts derived from green algae,10 though their story is more complicated than that of the euglenophytes. The ancestor of chlorarachniophytes is thought to have been a chromalveolate, a eukaryote with a red algal derived chloroplast. It's then thought to have lost its first red algal chloroplast, and later engulfed a green alga, giving it its second, green algal derived chloroplast.21
Chlorarachniophyte chloroplasts are bounded by four membranes, except near the cell membrane, where the chloroplast membranes fuse into a double membrane.8 Their thylakoids are arranged in loose stacks of three.8 Chlorarachniophytes have a form of starch called chrysolaminarin, which they store in the cytoplasm,21 often collected around the chloroplast pyrenoid, which bulges into the cytoplasm.8
Chlorarachniophyte chloroplasts are notable because the green alga they are derived from has not been completely broken down—its nucleus still persists as a nucleomorph10 found between the second and third chloroplast membranes8—the periplastid space, which corresponds to the green alga's cytoplasm.21
Recent research has suggested that the ancestor of the chromalveolates acquired a green algal prasinophyte endosymbiont. The green algal derived chloroplast was lost and replaced with a red algal derived chloroplast, but not before contributing some of its genes to the early chromalveolate's nucleus. The presence of both green algal and red algal genes in chromalveolates probably helps them thrive under fluctuating light conditions.29
Like green algae, red algae have also been taken up in secondary endosymbiosis, though it's thought that all red algal derived chloroplasts are descended from a single red alga that was engulfed by an early chromalveolate, giving rise to the chromalveolates, some of which, like the ciliates, subsequently lost the chloroplast.102122 This is still debated though.2122
Pyrenoids and stacked thylakoids are common in chromalveolate chloroplasts, and the outermost membrane of many are continuous with the rough endoplasmic reticulum and studded with ribosomes.821 They have lost their phycobilisomes and exchanged them for chlorophyll c, which isn't found in primary red algal chloroplasts themselves.8
Cryptophytes, or cryptomonads are a group of algae that contain a red-algal derived chloroplast. Cryptophyte chloroplasts contain a nucleomorph that superficially resembles that of the chlorarachniophytes.10 Cryptophyte chloroplasts have four membranes, the outermost of which is continuous with the rough endoplasmic reticulum. They synthesize ordinary starch, which is stored in granules found in the periplastid space—outside the original double membrane, in the place that corresponds to the red alga's cytoplasm. Inside cryptophyte chloroplasts is a pyrenoid and thylakoids in stacks of two.8
Haptophytes are similar and closely related to cryptophytes, and are thought to be the first chromalveolates to branch off.21 Their chloroplasts lack a nucleomorph,810 their thylakoids are in stacks of three, and they synthesize chrysolaminarin sugar, which they store completely outside of the chloroplast, in the cytoplasm of the haptophyte.8
The heterokontophytes, also known as the stramenopiles, are a very large and diverse group of algae that also contain red algal derived chloroplasts.21 Heterokonts include the diatoms and the brown algae, golden algae,22 and yellow-green algae.
Heterokont chloroplasts are very similar to haptophyte chloroplasts, containing a pyrenoid, triplet thylakoids, and with some exceptions,8 having an epiplastid membrane connected to the endoplasmic reticulum. Like haptophytes, heterokontophytes store sugar in chrysolaminarin granules in the cytoplasm.8 Heterokontophyte chloroplasts contain chlorophyll a and with a few exceptions8 chlorophyll c,10 but also have carotenoids which give them their many colors.22
Apicomplexans are another group of chromalveolates. Like the helicosproidia, they're parasitic, and have a nonphotosynthetic chloroplast.21 They were once thought to be related to the helicosproidia, but it is now known that the helicosproida are green algae rather than chromalveolates.21 The apicomplexans include Plasmodium, the malaria parasite. Many apicomplexans keep a vestigial red algal derived chloroplast2021 called an apicoplast, which they inherited from their ancestors. Other apicomplexans like Cryptosporidium have lost the chloroplast completely.20 Apicomplexans store their energy in amylopectin starch granules that are located in their cytoplasm, even though they are nonphotosynthetic.8
Apicoplasts have lost all photosynthetic function, and contain no photosynthetic pigments or true thylakoids. They are bounded by four membranes, but the membranes are not connected to the endoplasmic reticulum.8 The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other than photosynthesis. Plant chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesize fatty acids, isopentenyl pyrophosphate, iron-sulfur clusters, and carry out part of the heme pathway.20 This makes the apicoplast an attractive target for drugs to cure apicomplexan-related diseases.18 The most important apicoplast function is isopentenyl pyrophosphate synthesis—in fact, apicomplexans die when something interferes with this apicoplast function, and when apicomplexans are grown in an isopentenyl pyrophosphate-rich medium, they dump the organelle.20
Most dinophyte chloroplasts are secondary red algal derived chloroplasts, like other chromalveolate chloroplasts. Many other dinophytes have lost the chloroplast (becoming the nonphotosynthetic kind of dinoflagellate), or replaced it though tertiary endosymbiosis32—the engulfment of another chromalveolate containing a red algal derived chloroplast. Others replaced their original chloroplast with a green algal derived one.102131
Most dinophyte chloroplasts contain at least the photosynthetic pigments chlorophyll a, chlorophyll c2, beta-carotene, and at least one dinophyte-unique xanthophyll (peridinin, dinoxanthin, or diadinoxanthin), giving many a golden-brown color.31 All dinophytes store starch in their cytoplasm, and most have chloroplasts with thylakoids arranged in stacks of three.8
The most common dinophyte chloroplast is the peridinin-type chloroplast, characterized by the carotenoid pigment peridinin in their chloroplasts, along with chlorophyll a and chlorophyll c2.1031 Peridinin is not found in any other group of chloroplasts.31 The peridinin chloroplast is bounded by three membranes (occasionally two),8 having lost the red algal endosymbiont's original cell membrane.2110 The outermost membrane is not connected to the endoplasmic reticulum.831 They contain a pyrenoid, and have triplet-stacked thylakoids. Starch is found outside the chloroplast8 An important feature of these chloroplasts is that their chloroplast DNA is highly reduced and fragmented into many small circles. Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast.31
The fucoxanthin dinophyte lineages (including Karlodinium and Karenia)21 lost their original red algal derived chloroplast, and replaced it with a new chloroplast derived from a haptophyte endosymbiont. Karlodinium and Karenia probably took up different heterokontophytes.21 Because the haptophyte chloroplast has four membranes, tertiary endosymbiosis would be expected to create a six membraned chloroplast, adding the haptophyte's cell membrane and the dinophyte's phagosomal vacuole.34 However, the haptophyte was heavily reduced, stripped of a few membranes and its nucleus, leaving only its chloroplast (with its original double membrane), and possibly one or two additional membranes around it.2134
Fucoxanthin-containing chloroplasts are characterized by having the pigment fucoxanthin (actually 19′-hexanoyloxy-fucoxanthin and/or 19′-butanoyloxy-fucoxanthin) and no peridinin. Fucoxanthin is also found in haptophyte chloroplasts, providing evidence of ancestry.31
Members of the genus Dinophysis have a phycobilin-containing34 chloroplast taken from a cryptophyte.10 However, the cryptophyte is not an endosymbiont—only the chloroplast seems to have been taken, and the chloroplast has been stripped of its nucleomorph and outermost two membranes, leaving just a two-membraned chloroplast. Cryptophyte chloroplasts require their nucleomorph to maintain themselves, and Dinophysis species grown in cell culture alone cannot survive, so it's possible (but not confirmed) that the Dinophysis chloroplast is a kleptoplast—if so, Dinophysis chloroplasts wear out and Dinophysis species must continually engulf cryptophytes to obtain new chloroplasts to replace the old ones.31
Some dinophytes, like Kryptoperidinium and Durinskia21 have a diatom (heterokontophyte) derived chloroplast.10 These chloroplasts are bounded by up to five membranes,10 (depending on whether you count the entire diatom endosymbiont as the chloroplast, or just the red algal derived chloroplast inside it). The diatom endosymbiont has been reduced relatively little—it still retains its original mitochondria,21 and has endoplasmic reticulum, ribosomes, a nucleus, and of course, red algal derived chloroplasts—practically a complete cell,35 all inside the host's endoplasmic reticulum lumen.21 However the diatom endosymbiont can't store its own food—its starch is found in granules in the dinophyte host's cytoplasm instead.358 The diatom endosymbiont's nucleus is present, but it probably can't be called a nucleomorph because it shows no sign of genome reduction, and might have even been expanded.21 Diatoms have been engulfed by dinoflagellates at least three times.21
The diatom endosymbiont is bounded by a single membrane,31 inside it are chloroplasts with four membranes. Like in the diatom endosymbiont's diatom ancestor, the chloroplasts have triplet thylakoids and pyrenoids.35
In some of these genera, the diatom endosymbiont's chloroplasts aren't the only chloroplasts in the dinophyte. The original three-membraned peridinin chloroplast is still around, converted to an eyespot.1021
Lepidodinium viride and its close relatives are dinophytes that lost their original peridinin chloroplast and replaced it with a green algal derived chloroplast (more specifically, a prasinophyte).318 Lepidodinium is the only dinophyte that has a chloroplast that's not from the rhodoplast lineage. The chloroplast is surrounded by two membranes and has no nucleomorph—all the nucleomorph genes have been transferred to the dinophyte nucleus.31 The endosymbiotic event that led to this chloroplast was serial secondary endosymbiosis rather than tertiary endosymbiosis—the endosymbiont was a green alga containing a primary chloroplast (making a secondary chloroplast).21
While most chloroplasts originate from that first set of endosymbiotic events, Paulinella chromatophora is an exception, which has acquired a photosynthetic cyanobacterial endosymbiont more recently. It is not closely related to chloroplasts of other eukaryotes.36 Being in the early stages of endosymbiosis, Paulinella chromatophora can offer some insights into how chloroplasts evolved.1537 Paulinella cells contain one or two sausage shaped blue-green photosynthesizing structures called chromatophores,1537 descended from the cyanobacterium Synechococcus. Chromatophores cannot survive outside their host.15 Chromatophore DNA is about a million base pairs long, containing around 850 protein encoding genes—far less than the three million base pair Synechococcus genome,15 but much larger than the ~150,000 base pair genome of the more assimilated chloroplast.383940 Chromatophores have transferred much less of their DNA to the nucleus of their host. About 0.3–0.8% of the nuclear DNA in Paulinella is from the chromatophore, compared with 11–14% from the chloroplast in plants.37
In some groups of mixotrophic protists, like some dinoflagellates, chloroplasts are separated from a captured alga or diatom and used temporarily. These klepto chloroplasts may only have a lifetime of a few days and are then replaced.41
Chloroplasts have their own DNA,42 often abbreviated as ctDNA,43 or cpDNA.44 It is also known as the plastome. Its existence was first proved in 1962,38 and first sequenced in 1986—when two Japanese research teams sequenced the chloroplast DNA of liverwort and tobacco.45 Since then, hundreds of chloroplast DNAs from various species have been sequenced, but they're mostly those of land plants and green algae—glaucophytes, red algae, and other algal groups are extremely underrepresented, potentially introducing some bias in views of "typical" chloroplast DNA structure and content.46
Most chloroplasts have their entire chloroplast genome combined into a single large ring, though those of dinophyte algae are a notable exception—their genome is broken up into about forty small plasmids, each 2,000–10,000 base pairs long.46 Each minicircle contains one to three genes,1646 but blank plasmids, with no coding DNA, have also been found.
Many chloroplast DNAs contain two inverted repeats, which separate a long single copy section (LSC) from a short single copy section (SSC).40
The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 base pairs long each.46 Inverted repeats in plants tend to be at the upper end of this range, each being 20,000–25,000 base pairs long.4048 The inverted repeat regions usually contain three ribosomal RNA and two tRNA genes, but they can be expanded or reduced to contain as few as four or as many as over 150 genes.46 While a given pair of inverted repeats are rarely completely identical, they are always very similar to each other, apparently resulting from concerted evolution.46
The inverted repeat regions are highly conserved among land plants, and accumulate few mutations.4048 Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages (glaucophyta and rhodophyceæ), suggesting that they predate the chloroplast,46 though some chloroplast DNAs like those of peas and a few red algae46 have since lost the inverted repeats.4849 Others, like the red alga Porphyra flipped one of its inverted repeats (making them direct repeats).46 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.49
Chloroplast DNAs have long been thought to have a circular structure, but some evidence suggests that chloroplast DNA more commonly takes a linear shape.50 Over 95% of the chloroplast DNA in corn chloroplasts has been observed to be in branched linear form rather than individual circles.46
New chloroplasts may contain up to 100 copies of their DNA,38 though the number of chloroplast DNA copies decreases to about 15–20 as the chloroplasts age.51 They are usually packed into nucleoids which can contain several identical chloroplast DNA rings. Many nucleoids can be found in each chloroplast.47
Though chloroplast DNA is not associated with true histones,3 in red algae, a histone-like chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast DNA ring into a nucleoid has been found.52
The chloroplast genome most commonly includes around 100 genes1639 which code for a variety of things, mostly to do with the protein pipeline and photosynthesis. As in prokaryotes, genes in chloroplast DNA are organized into operons.16
Among land plants, the contents of the chloroplast genome are fairly similar40—they code for four ribosomal RNAs, 30–31 tRNAs, 21 ribosomal proteins, and four RNA polymerase subunits,5354 involved in protein synthesis. For photosynthesis, the chloroplast DNA includes genes for 28 thylakoid proteins and the large Rubisco subunit.53 In addition, its genes encode eleven subunits of a protein complex which mediates redox reactions to recycle electrons,55 which is similar to the NADH dehydrogenase found in mitochondria.5356
Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host,383957 a process called endosymbiotic gene transfer. As a result, the chloroplast genome is heavily 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.58
Endosymbiotic gene transfer is how we know about the lost chloroplasts in many 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 (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 (probably the ancestor of all chromalveolates too) had a green algal derived chloroplast at some point, which was subsequently replaced by the red chloroplast.29
In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast,37 up to 18% in Arabidopsis, corresponding to about 4,500 protein-coding genes.59 There have been a few recent transfers of genes from the chloroplast DNA to the nuclear genome in land plants.39
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 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.60
Protein synthesis within chloroplasts relies on an 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 within the chloroplast genome.61 The ribosomes in chloroplasts are similar to bacterial ribosomes.53
|This section requires expansion with: Genome size differences between algae and land plants, chloroplast stuff coded by the nucleus, DNA replication, NADPH redox, special tRNA synthetases, etc.. (January 2013)|
|This section requires expansion. (June 2013)|
The movement of so many chloroplast genes to the nucleus means that lots of chloroplast proteins that were supposed to be translated 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.62
Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many became exaptations, taking on new functions like participating in cell division, protein routing, and even disease resistance. A few chloroplast genes found new homes in the mitochondrial genome—most became nonfunctional pseudogenes, though a few tRNA genes still work in the mitochondrion.58 Some transferred chloroplast DNA protein products get directed to the secretory pathway58 (though it should be noted that many secondary plastids are bounded by an outermost membrane derived from the host's cell membrane, and therefore topologically outside of the cell, because to reach the chloroplast from the cytosol, you have to cross the cell membrane, just like if you were headed for the extracellular space. In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway).21
Because the cell acquiring a chloroplast already had mitochondria (and peroxisomes, and a cell membrane for secretion), the new chloroplast host had to develop a unique protein targeting system to avoid having chloroplast proteins being sent to the wrong organelle, and the wrong proteins being sent to the chloroplast.62
Polypeptides, the precursors of proteins, are chains of amino acids. The two ends of a polypeptide are called the N-terminus, or amino end, and the C-terminus, or carboxyl end.63 For many (but not all) chloroplast proteins encoded by nuclear genes, cleavable transit peptides are added to the N-termini of the polypeptides, which are used to help direct the polypeptide to the chloroplast for import6264 (N-terminal transit peptides are also used to direct polypeptides to plant mitochondria).65 N-terminal transit sequences are also called presequences62 because they are located at the "front" end of a polypeptide—ribosomes synthesize polypeptides from the N-terminus to the C-terminus.63
Chloroplast transit peptides exhibit huge variation in length and amino acid sequence.64 They can be from 20–150 amino acids long62—an unusually long length, suggesting that transit peptides are actually collections of domains with different functions.64 Transit peptides tend to be positively charged,62 rich in hydroxylated amino acids such as serine, threonine, and proline, and poor in acidic amino acids like aspartic acid and glutamic acid.64 In an aqueous solution, the transit sequence forms a random coil.62
Not all chloroplast proteins include a N-terminal cleavable transit peptide though.62 Some include the transit sequence within the functional part of the protein itself.62 A few have their transit sequence appended to their C-terminus instead.66 Most of the polypeptides that lack N-terminal targeting sequences are the ones that are sent to the outer chloroplast membrane, plus at least one sent to the inner chloroplast membrane.62
After a chloroplast polypeptide is synthesized on a ribosome in the cytosol, ATP energy can be used to phosphorylate, or add a phosphate group to many (but not all) of them in their transit sequences.62 Serine and threonine (both very common in chloroplast transit sequences—making up 20–30% of the sequence)67 are often the amino acids that accept the phosphate group.6765 The enzyme that carries out the phosphorylation is specific for chloroplast polypeptides, and ignores ones meant for mitochondria or peroxisomes.67
Phosphorylation changes the polypeptide's shape,67 making it easier for 14-3-3 proteins to attach to the polypeptide.6268 In plants, 14-3-3 proteins only bind to chloroplast preproteins.65 It is also bound by the heat shock protein Hsp70 that keeps the polypeptide from folding prematurely.62 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.6568 At the same time, they have to keep just enough shape so that they can be recognized and imported into the chloroplast.65
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.62
Alternatively, if its transit peptide is not phosphorylated, a chloroplast preprotein can still attach to a heat shock protein or TOC159. These complexes can bind to the TOC complex on the outer chloroplast membrane using GTP energy.62
|This section requires expansion. (June 2013)|
The TOC complex, or translocon on the outer chloroplast membrane, is a collection of proteins that imports preproteins across the outer chloroplast envelope. Four subunits of the TOC complex have been identified—two GTP-binding proteins Toc34 and Toc159, the protein import tunnel Toc75, plus the protein Toc64.62
Toc34 is an integral protein in the outer chloroplast membrane that's anchored into it by its C-terminal tail.6268 Most of the protein, however, including its large guanosine triphosphate (GTP)-binding domain projects out into the stroma.68
Toc34's job is to catch some chloroplast preproteins in the cytosol and hand them off to the rest of the TOC complex.62 When GTP, an energy molecule similar to ATP attaches to Toc34, the protein becomes much more able to bind to many chloroplast preproteins in the cytosol.62 The chloroplast preprotein's presence causes Toc34 to break GTP into guanosine diphosphate (GDP) and inorganic phosphate. This loss of GTP makes the Toc34 protein release the chloroplast preprotein, handing it off to the next TOC protein.62 Toc34 then releases the depleted GDP molecule, probably with the help of an unknown GDP exchange factor. A domain of 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.62
Toc34 can be turned off through phosphorylation. A protein kinase drifting around on the outer chloroplast membrane can use ATP to add a phosphate group to the Toc34 protein, preventing it from being able to receive another GTP molecule, inhibiting the protein's activity. This might provide a way to regulate protein import into chloroplasts.6268
Arabidopsis thaliana has two homologous proteins, AtToc33 and AtToc34 (The At stands for Arabidopsis thaliana),6268 which are each about 60% identical in amino acid sequence to Toc34 in peas (called psToc34).68 AtToc33 is the most common in Arabidopsis,68 and it's the functional analogue of Toc34 because it can be turned off by phosphorylation. AtToc34 on the other hand cannot be phosphorylated.6268
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In land plants, chloroplasts are generally lens-shaped, 5–8 μm in diameter and 1–3 μm thick.70 Greater diversity in chloroplast shapes exists among the algae, which often contain a single chloroplast8 that can be shaped like a net (e.g., Oedogonium),71 a cup (e.g., Chlamydomonas),72 a ribbon-like spiral around the edges of the cell (e.g., Spirogyra),73 or slightly twisted bands at the cell edges (e.g., Sirogonium).74 Some algae have two chloroplasts in each cell; they are star-shaped in Zygnema,75 or may follow the shape of half the cell in order Desmidiales.76 In some algae, the chloroplast takes up most of the cell, with pockets for the nucleus and other organelles8 (for example some species of Chlorella have a cup-shaped chloroplast that occupies much of the cell).77
All chloroplasts have at least three membrane systems—the outer chloroplast membrane, the inner chloroplast membrane, and the thylakoid system. Chloroplasts that are the product of secondary endosymbiosis may have additional membranes surrounding these three.28 Inside the outer and inner chloroplast membranes is the chloroplast stroma, a semi-gel-like fluid18 that makes up much of a chloroplast's volume, and in which the thylakoid system floats.
Chloroplast ultrastructure Chloroplasts have at least three distinct membrane systems, and a variety of things can be found in their stroma.
There are some common misconceptions about the outer and inner chloroplast membranes. The fact that chloroplasts are surrounded by a double membrane is often cited as evidence that they are the descendants of endosymbiotic cyanobacteria. This is often interpreted as meaning the outer chloroplast membrane is the product of the host's cell membrane infolding to form a vesicle to surround the ancestral cyanobacterium—which is not true—both chloroplast membranes are homologous to the cyanobacterium's original double membranes.10
The chloroplast double membrane is also often compared to the mitochondrial double membrane. This is not a valid comparison—the inner mitochondria membrane is used to run proton pumps and carry out oxidative phosphorylation across to generate ATP energy. The only chloroplast structure that can considered analogous to it is the internal thylakoid system. Even so, in terms of "in-out", the direction of chloroplast H+ ion flow is in the opposite direction compared to oxidative phosphorylation in mitochondria.1878 In addition, in terms of function, the inner chloroplast membrane, which regulates metabolite passage and synthesizes some materials, has no counterpart in the mitochondrion.18
The outer chloroplast membrane is a semi-porous membrane that small molecules and ions can easily diffuse across.79 However, it's not permeable to larger proteins, so chloroplast polypeptides being synthesized in the cell cytoplasm must be transported across the outer chloroplast membrane by the TOC complex, or translocon on the outer chloroplast membrane.80
The chloroplast membranes sometimes protrude out into the cytoplasm, forming a stromule, or stroma-containing tubule. Stromules are very rare in chloroplasts, and are much more common in other plastids like chromoplasts and amyloplasts in petals and roots, respectively.8182 They may exist to increase the chloroplast's surface area for cross-membrane transport, connect two or more chloroplasts allowing them to exchange metabolites, or both.18
Glaucophyte algal chloroplasts have a peptidoglycan layer between the chloroplast membranes. It corresponds to the peptidoglycan cell wall of their cyanobacterial ancestors, which is located between their two cell membranes. These chloroplasts are called muroplasts (from Latin "mura", meaning "wall"). Other chloroplasts have lost the cyanobacterial wall, leaving an intermembrane space between the two chloroplast envelope membranes.18
The inner chloroplast membrane borders the stroma and regulates passage of materials in and out of the chloroplast. After passing through the TOC complex in the outer chloroplast membrane, polypeptides must pass through the TIC complex (translocon on the inner chloroplast membrane) which is located in the inner chloroplast membrane.80
Some chloroplasts contain a structure called the chloroplast peripheral reticulum.83 It is often found in the chloroplasts of C4 plants, though it's also been found in some C3 angiosperms,18 and even some gymnosperms.84 The chloroplast peripheral reticulum consists of a maze of membranous tubes and vesicles continuous with the inner chloroplast membrane that extends into the internal stromal fluid of the chloroplast. Its purpose is thought to be to increase the chloroplast's surface area for cross-membrane transport between its stroma and the cell cytoplasm. The small vesicles sometimes observed may serve as transport vesicles to shuttle stuff between the thylakoids and intermembrane space.85
The protein-rich,18 alkaline,78 aqueous fluid within the inner chloroplast membrane and outside of the thylakoid space is called the stroma,18 which corresponds to the cytosol of the original cyanobacterium. Nucleoids of chloroplast DNA, chloroplast ribosomes, the thylakoid system with plastoglobuli, starch granules, and many proteins can be found floating around in it. The Calvin cycle, which fixes CO2 into sugar takes place in the stroma.
Chloroplast ribosomes Comparison of a chloroplast ribosome (green) and a bacterial ribosome (yellow). Important features common to both ribosomes and chloroplast-unique features are labeled.
Chloroplasts have their own ribosomes, which they use to synthesize a small fraction of their proteins. Chloroplast ribosomes are about two-thirds the size of cytoplasmic ribosomes (around 17 nm vs 25 nm).83 They take mRNAs transcribed from the chloroplast DNA and translate them into protein. While similar to bacterial ribosomes,3 chloroplast translation is more complex than in bacteria, so chloroplast ribosomes include some chloroplast-unique features.86
Plastoglobuli (singular plastoglobulus, sometimes spelled plastoglobule(s)), are spherical globules of lipids and proteins18 about 10–15 nanometers across.83 They are surrounded by a lipid monolayer.87 Plastoglobuli are found in all chloroplasts,83 but become more common when the chloroplast is under oxidative stress,87 or when it ages and transitions into a gerontoplast.18 They are also common in etioplasts, but decrease in number as the etioplasts mature into chloroplasts.87
Plastoglobuli were once thought to be free-floating in the stroma, but it is now thought that they are permanently attached either to a thylakoid or to another plastoglobulus attached to a thylakoid. Plastoglubuli contain both structural proteins and enzymes involved in lipid synthesis and metabolism. They can form when a bubble appears between the layers of the lipid bilayer of the thylakoid membrane, or bud from existing plastoglubuli—though they never detach and float off into the stroma.87
Starch granules are very common in chloroplasts, typically taking up 15% of the organelle's volume,88 though in some other plastids like amyloplasts, they can be big enough to distort the shape of the organelle.83 Starch granules are simply accumulations of starch in the stroma, and are not bounded by a membrane.83
Starch granules appear and grow throughout the day, as the chloroplast synthesizes sugars, and are consumed at night to fuel respiration and continue sugar export into the phloem,89 though in mature chloroplasts, it's rare for a starch granule to be completely consumed or for a new granule to accumulate.88
Starch granules vary in composition and location across different chloroplast lineages. In red algae, starch granules are found in the cytoplasm rather than in the chloroplast.90 In C4 plants, mesophyll chloroplasts, which do not synthesize sugars, lack starch granules.18
The chloroplast stroma contains many proteins, though the most common and important is Rubisco, which is probably also the most abundant protein on the planet.78 Rubisco is the enzyme that fixes CO2 into sugar molecules. In C3 plants, rubisco is abundant in all chloroplasts, though in C4 plants, it's confined to the bundle sheath chloroplasts, where the Calvin cycle is carried out in C4 plants.91
The chloroplasts of some hornworts92 and algae contain structures called pyrenoids. They are not found in higher plants.93 Pyrenoids are roughly spherical and highly refractive bodies which are a site of starch accumulation in plants that contain them. They consist of an matrix opaque to electrons, surrounded by two hemispherical starch plates. The starch is accumulated as the pyrenoids mature.94 In algae with carbon concentrating mechanisms, the enzyme rubisco is found in the pyrenoids. Starch can also accumulate around the pyrenoids when CO2 is scarce.93 Pyrenoids can divide to form new pyrenoids, or be produced "de novo".9495
Suspended within the chloroplast stroma is the thylakoid system, a highly dynamic collection of membranous sacks called thylakoids where chlorophyll is found and the light reactions of photosynthesis happen.7 In most vascular plant chloroplasts, the thylakoids are arranged in stacks called grana,96 though in certain C4 plant chloroplasts91 and some algal chloroplasts, the thylakoids are free floating.8
Using a light microscope, it's just barely possible to see tiny green granules—which were named grana.83 With electron microscopy, it became possible to see the thylakoid system in more detail, revealing it to consist of stacks of flat thylakoids which made up the grana, and long interconnecting stromal thylakoids which linked different grana.83 In the transmission electron microscope, thylakoid membranes appear as alternating light-and-dark bands, 8.5 nanometers thick.83
For a long time, the three dimensional structure of the thylakoid system has been unknown or disputed. One model has the granum as a stack of thylakoids linked by helical stromal thylakoids; the other has the granum as a single folded thylakoid connected in a "hub and spoke" way to other grana by stromal thylakoids. While the thylakoid system is still commonly depicted according to the folded thylakoid model,7 it was determined in 2011 that the stacked and helical thylakoids model is correct.97
In the helical thylakoid model, grana consist of a stack of flattened circular granal thylakoids that resemble pancakes. Each granum can contain anywhere from two to a hundred thylakoids,83 though grana with 10–20 thylakoids are most common.96 Wrapped around the grana are helicoid stromal thylakoids, also known as frets or lamellar thylakoids. The helices ascend at an angle of 20–25°, connecting to each granal thylakoid at a bridge-like slit junction. The helicoids may extend as large sheets that link multiple grana, or narrow to tube-like bridges between grana.97 While different parts of the thylakoid system contain different membrane proteins, the thylakoid membranes are continuous and the thylakoid space they enclose form a single continuous labyrinth.96
Thylakoids (sometimes spelled thylakoïds),98 are small interconnected sacks which contain the membranes that the light reactions of photosynthesis take place on. The word thylakoid comes from the Greek word thylakos which means "sack".99
Embedded in the thylakoid membranes are important protein complexes which carry out the light reactions of photosynthesis. Photosystem II and photosystem I contain light-harvesting complexes with chlorophyll and carotenoids that absorb light energy and use it to energize electrons. Molecules in the thylakoid membrane use the energized electrons to pump hydrogen ions into the thylakoid space, decreasing the pH and turning it acidic. ATP synthase is a large protein complex that harnesses the concentration gradient of the hydrogen ions in the thylakoid space to generate ATP energy as the hydrogen ions flow back out into the stroma—much like a dam turbine.78
There are two types of thylakoids—granal thylakoids, which are arranged in grana, and stromal thylakoids, which are in contact with the stroma. Granal thylakoids are pancake-shaped circular disks about 300–600 nanometers in diameter. Stromal thylakoids are helicoid sheets that spiral around grana.96 The flat tops and bottoms of granal thylakoids contain only the relatively flat photosystem II protein complex. This allows them to stack tightly, forming grana with many layers of tightly appressed membrane, called granal membrane, increasing stability and surface area for light capture.96
In contrast, photosystem I and ATP synthase are large protein complexes which jut out into the stroma. They can't fit in the appressed granal membranes, and so are found in the stromal thylakoid membrane—the edges of the granal thylakoid disks and the stromal thylakoids. These large protein complexes may act as spacers between the sheets of stromal thylakoids.96
The number of thylakoids and the total thylakoid area of a chloroplast is influenced by light exposure. Shaded chloroplasts contain larger and more grana with more thylakoid membrane area than chloroplasts exposed to bright light, which have smaller and fewer grana and less thylakoid area. Thylakoid extent can change within minutes of light exposure or removal.85
Inside the photosystems embedded in chloroplast thylakoid membranes are various photosynthetic pigments, which absorb and transfer light energy. The types of pigments found are different in various groups of chloroplasts, and are responsible for a wide variety of chloroplast colorations.
Chlorophyll a is found in all chloroplasts, as well as their cyanobacterial ancestors. Chlorophyll a is a blue-green pigment100 partially responsible for giving most cyanobacteria and chloroplasts their color. Other forms of chlorophyll exist, such as the accessory pigments chlorophyll b, chlorophyll c, chlorophyll d,8 and chlorophyll f.
Chlorophyll b is an olive green pigment found only in the chloroplasts of plants, green algae, any secondary chloroplasts obtained through the secondary endosymbiosis of a green alga, and a few cyanobacteria.8 It's the chlorophylls a and b together that make most plant and green algal chloroplasts green.100
Chlorophyll c is mainly found in secondary endosymbiotic chloroplasts that originated from a red alga, though it's not found in chloroplasts of red algae themselves. Chlorophyll c is also found in some green algae and cyanobacteria.8
In addition to chlorophylls, another group of yellow–orange100 pigments called carotenoids are also found in the photosystems. There are about thirty photosynthetic carotenoids.102 They help transfer and dissipate excess energy,8 and their bright colors sometimes override the chlorophyll green, like during the fall, when the leaves of some land plants change color.103 β-carotene is a bright red-orange carotenoid found in nearly all chloroplasts, like chlorophyll a.8 Xanthophylls, especially the orange-red zeaxanthin, are also common.102 Many other forms of carotenoids exist that are only found in certain groups of chloroplasts.8
Phycobilins are a third group of pigments found in cyanobacteria, and glaucophyte, red algal, and cryptophyte chloroplasts.8104 Phycobilins come in all colors, though phycoerytherin is one of the pigments that makes many red algae red.105 Phycobilins often organize into relatively large protein complexes about 40 nanometers across called phycobilisomes.8 Like photosystem I and ATP synthase, phycobilisomes jut into the stroma, preventing thylakoid stacking in red algal chloroplasts.8 Cryptophyte chloroplasts and some cyanobacteria don't have their phycobilin pigments organized into phycobilisomes, and keep them in their thylakoid space instead.8
To fix carbon dioxide into sugar molecules in the process of photosynthesis, chloroplasts use an enzyme called rubisco. Rubisco has a problem—it has trouble distinguishing between carbon dioxide and oxygen, so at high oxygen concentrations, rubisco starts accidentally adding oxygen to sugar precursors. This has the end result of ATP energy being wasted and CO2 being released, all with no sugar being produced. This is a big problem, since O2 is produced by the initial light reactions of photosynthesis, causing issues down the line in the Calvin cycle which uses rubisco.106
C4 plants evolved a way to solve this—by spatially separating the light reactions and the Calvin cycle. The light reactions, which store light energy in ATP and NADPH, are done in the mesophyll cells of a C4 leaf. The Calvin cycle, which uses the stored energy to make sugar using rubisco, is done in the bundle sheath cells, a layer of cells surrounding a vein in a leaf.106
As a result, chloroplasts in C4 mesophyll cells and bundle sheath cells are specialized for each stage of photosynthesis. In mesophyll cells, chloroplasts are specialized for the light reactions, so they lack rubisco, and have normal grana and thylakoids,91 which they use to make ATP and NADPH, as well as oxygen. They store CO2 in a four-carbon compound, which is why the process is called C4 photosynthesis. The four-carbon compound is then transported to the bundle sheath chloroplasts, where it drops off CO2 and returns to the mesophyll. Bundle sheath chloroplasts do not carry out the light reactions, preventing oxygen from building up in them and disrupting rubisco activity.106 Because of this, they lack thylakoids organized into grana stacks—though bundle sheath chloroplasts still have free-floating thylakoids in the stroma where they still carry out cyclic electron flow, a light-driven method of synthesizing ATP to power the Calvin cycle without generating oxygen. They lack photosystem II, and only have photosystem I—the only protein complex needed for cyclic electron flow.91106 Because the job of bundle sheath chloroplasts is to carry out the Calvin cycle and make sugar, they often contain large starch grains.91
Both types of chloroplast contain large amounts of chloroplast peripheral reticulum,91 which they use to get more surface area to transport stuff in and out of them.8485 Mesophyll chloroplasts have a little more peripheral reticulum than bundle sheath chloroplasts.107
Not all cells in a multicellular plant contain chloroplasts. All green parts of a plant contain chloroplasts—the chloroplasts, or more specifically, the chlorophyll in them are what make the photosynthetic parts of a plant green.7 The plant cells which contain chloroplasts are usually parenchyma cells, though chloroplasts can also be found in collenchyma tissue.108 A plant cell which contains chloroplasts is known as a chlorenchyma cell. A typical chlorenchyma cell of a land plant contains about 10 to 100 chloroplasts.
A cross section of a leaf, showing chloroplasts in its mesophyll cells. Stomal guard cells also have chloroplasts, though much fewer than mesophyll cells.
In some plants such as cacti, chloroplasts are found in the stems,109 though in most plants, chloroplasts are concentrated in the leaves. One square millimeter of leaf tissue can contain half a million chloroplasts.7 Within a leaf, chloroplasts are mainly found in the mesophyll layers of a leaf, and the guard cells of stomata. Palisade mesophyll cells can contain 30–70 chloroplasts per cell, while stomatal guard cells contain only around 8–15 per cell, as well as much less chlorophyll. Chloroplasts can also be found in the bundle sheath cells of a leaf, especially in C4 plants, which carry out the Calvin cycle in their bundle sheath cells. They are often absent from the epidermis of a leaf.110
The chloroplasts of plant and algal cells can orient themselves to best suit the available light. In low-light conditions, they will spread out in a sheet—maximizing the surface area to absorb light. Under intense light, they will seek shelter by aligning in vertical columns along the plant cell's cell wall or turning sideways so that light strikes them edge-on. This reduces exposure and protects them from photooxidative damage.111 This ability to distribute chloroplasts so that they can take shelter behind each other or spread out may be the reason why land plants evolved to have many small chloroplasts instead of a few big ones,112 Chloroplast movement is considered one of the most closely regulated stimulus-response systems that can be found in plants.113 Mitochondria have also been observed to follow chloroplasts as they move.114
In higher plants, chloroplast movement is run by phototropins, blue light photoreceptors also responsible for plant phototropism. In some algae, mosses, ferns, and flowering plants, chloroplast movement is influenced by red light in addition to blue light,111 though very long red wavelengths inhibit movement rather than speeding it up. Blue light generally causes chloroplasts to seek shelter, while red light draws them out to maximize light absorption.114
Studies of Vallisneria gigantea, an aquatic flowering plant, have shown that chloroplasts can get moving within five minutes of light exposure, though they don't initially show any net directionality. They may move along microfilament tracks, and the fact that the microfilament mesh changes shape to form a honeycomb structure surrounding the chloroplasts after they have moved suggests that microfilaments may help to anchor chloroplasts in place.113114
Plants lack specialized immune cells—all plant cells participate in the plant immune response. Chloroplasts, along with the nucleus, cell membrane, and endoplasmic reticulum,115 are key players in pathogen defense. Due to its role in a plant cell's immune response, pathogens frequently target the chloroplast.115
Plants have two main immune responses—the hypersensitive response, in which infected cells seal themselves off and undergo programmed cell death, and systemic acquired resistance, where infected cells release signals warning the rest of the plant of a pathogen's presence. Chloroplasts stimulate both responses by purposely damaging their photosynthetic system, producing reactive oxygen species. High levels of reactive oxygen species will cause the hypersensitive response. The reactive oxygen species also directly kill any pathogens within the cell. Lower levels of reactive oxygen species initiate systemic acquired resistance, triggering defense-molecule production in the rest of the plant.115
Chloroplasts can serve as cellular sensors. After detecting stress in a cell, which might be due to a pathogen, chloroplasts begin producing molecules like salicylic acid, jasmonic acid, nitric oxide and reactive oxygen species which can serve as defense-signals. As cellular signals, reactive oxygen species are unstable molecules, so they probably don't leave the chloroplast, but instead pass on their signal to an unknown second messenger molecule. All these molecules initiate retrograde signaling—signals from the chloroplast that regulate gene expression in the nucleus.115
In addition to defense signaling, chloroplasts, with the help of the peroxisomes,116 help synthesize an important defense molecule, jasmonate. Chloroplasts synthesize all the fatty acids in a plant cell115117—linoleic acid, a fatty acid, is a precursor to jasmonate.115
One of the most important function of the chloroplast is carrying out photosynthesis to make food in the form of sugars for an alga or plant. Water (H2O) and carbon dioxide (CO2) are used in photosynthesis, and sugar and oxygen (O2) is made, using light energy. Photosynthesis is divided into two stages—the light reactions, where water is split to produce oxygen, and the dark reactions, or Calvin cycle, which builds sugar molecules from carbon dioxide. The two phases are linked by the energy carriers adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADP+).118
ATP is the phosphorylated version of adenosine diphosphate (ADP), which stores energy in a cell and powers most cellular activities. ATP is the energized form, while ADP is the (partially) depleted form. NADP+ is an electron carrier which ferries high energy electrons. In the light reactions, it gets reduced, meaning it picks up electrons, becoming NADPH.
Like mitochondria, chloroplasts use the potential energy stored in an H+, or hydrogen ion gradient to generate ATP energy. The two photosystems capture light energy to energize electrons taken from water, and release them down an electron transport chain. The molecules between the photosystems harness the electrons' energy to pump hydrogen ions into the thylakoid space, creating a concentration gradient, with more hydrogen ions (up to a thousand times as many)78 inside the thylakoid system than in the stroma. The hydrogen ions in the thylakoid space then diffuse back down their concentration gradient, flowing back out into the stroma through ATP synthase. ATP synthase uses the energy from the flowing hydrogen ions to phosphorylate adenosine diphosphate into adenosine triphosphate, or ATP.78 Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there, in position to be used in the dark reactions.119
Electrons are often removed from the electron transport chains to charge NADP+ with electrons, reducing it to NADPH. Like ATP synthase, ferredoxin-NADP+ reductase, the enzyme that reduces NADP+, releases the NADPH it makes into the stroma, right where it's needed for the dark reactions.119
Because NADP+ reduction removes electrons from the electron transport chains, they must be replaced—the job of photosystem II, which splits water molecules (H2O) to obtain the electrons from its hydrogen atoms.78118
While photosystem II photolyzes water to obtain and energize new electrons, photosystem I simply reenergizes depleted electrons at the end of an electron transport chain. Normally, the reenergized electrons are taken by NADP+, though sometimes they can flow back down more H+-pumping electron transport chains to transport more hydrogen ions into the thylakoid space to generate more ATP. This is termed cyclic photophosphorylation because the electrons are recycled. Cyclic photophosphorylation is common in C4 plants, which need more ATP than NADPH.106
The Calvin cycle (Interactive diagram) The Calvin cycle incorporates carbon dioxide into sugar molecules.
The Calvin cycle, also known as the dark reactions, is a series of biochemical reactions that fixes CO2 into G3P sugar molecules and uses the energy and electrons from the ATP and NADPH made in the light reactions. The Calvin cycle takes place in the stroma of the chloroplast.106
While named "the dark reactions", in most plants, they take place in the light, since the dark reactions are dependent on the products of the light reactions.7
The Calvin cycle starts by using the enzyme Rubisco to fix CO2 into five-carbon Ribulose bisphosphate (RuBP) molecules. The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called 3-phosphoglyceric acid, or 3-PGA. The ATP and NADPH made in the light reactions is used to convert the 3-PGA into glyceraldehyde-3-phosphate, or G3P sugar molecules. Most of the G3P molecules are recycled back into RuBP using energy from more ATP, but one out of every six produced leaves the cycle—the end product of the dark reactions.106
Glyceraldehyde-3-phosphate can double up and form glucose-1-phosphate, glucose-6-phosphate or fructose-6-phosphate molecules which each include a phosphate group. To synthesize sucrose, a disaccharide commonly known as table sugar, the G3P molecules are first transported into the cytoplasm by a translocon in the chloroplast membrane. In the cytoplasm, they double up to form fructose-6-phosphate, join with glucose monomers, and have their phosphate groups removed to become the disaccharide sucrose.120
Under conditions such as high atmospheric CO2 concentrations, large starch grains may form in the chloroplasts, distorting the grana and thylakoids. The starch granules displace the thylakoids, but leave them intact.121
Waterlogged roots can also cause starch buildup in the chloroplasts, possibly due to less sugar being exported through the phloem. This depletes a plant's free phosphate supply, which indirectly stimulates chloroplast starch synthesis.121 While linked to low photosynthesis rates, the starch grains themselves may not necessarily interfere significantly with the efficiency of photosynthesis,122 and might simply be a side effect of another photosynthesis-depressing factor.121
Photorespiration can occur when the oxygen concentration is too high. Rubisco cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O2 instead of CO2 to RuBP. This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO2, and produces no sugar. It can waste up to half the carbon fixed by the Calvin cycle.118 Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. These mechanisms are called carbon dioxide concentrating mechanisms, or CCMs. These include Crassulacean acid metabolism, C4 carbon fixation,118 and pyrenoids. Chloroplasts in C4 plants are notable as they exhibit a distinct chloroplast dimorphism.
Because of the H+ gradient across the thylakoid membrane, the interior of the thylakoid is acidic, with a pH around 4,123 while the stroma is slightly basic, with a pH of around 8.124 The optimal stroma pH for the Calvin cycle is 8.1, with the reaction nearly stopping when the pH falls below 7.3.125
CO2 in water can form carbonic acid, which can disturb the pH of isolated chloroplasts, interfering with photosynthesis, even though CO2 is used in photosynthesis. However, chloroplasts in living plant cells are not affected by this as much.124
In the presence of light, the pH of the thylakoid lumen can drop up to 1.5 pH units, while the pH of the stroma can rise by nearly one pH unit.125
|This section requires expansion with: needs more about lipids, also paramylon. (March 2013)|
Plants contain many different kinds of plastids in their cells.
Chloroplasts are a special type of plant cell organelle called a plastid, though the two terms are sometimes used interchangeably. There are many other types of plastids, which carry out various functions. All chloroplasts in a plant are descended from undifferentiated proplastids found in the zygote,127 or fertilized egg. Proplastids are commonly found in an adult plant's apical meristems. Chloroplasts do not normally develop from proplastids in root tip meristems128—instead, the formation of starch-storing amyloplasts is more common.127
In shoots, proplastids from shoot apical meristems gradually develop into chloroplasts in photosynthetic leaf tissues as the leaf matures, if exposed to the required light. This process involves invaginations of the inner plastid membrane, forming sheets of membrane that project into the internal stroma. These membrane sheets then fold to form thylakoids and grana.129
If angiosperm shoots are not exposed to the required light for chloroplast formation, proplastids may develop into an etioplast stage before becoming chloroplasts. An etioplast is a plastid that lacks chlorophyll, and has inner membrane invaginations that form a lattice of tubes in their stroma, called a prolamellar body. Within a few minutes of light exposure, the prolamellar body begins to reorganize into stacks of thylakoids, and chlorophyll starts to be produced. This process, where the etioplast becomes a chloroplast, takes several hours.129 Gymnosperms do not require light to form chloroplasts.129
Light, however, does not guarantee that a proplastid will develop into a chloroplast—what type of plastid a proplastid becomes is largely influenced by the kind of cell it resides in.127
Many plastid interconversions are possible.
Plastid differentiation is not permanent, in fact many interconversions are possible. Chloroplasts may be converted to chromoplasts, which are pigment-filled plastids responsible for the bright colors you see in flowers and ripe fruit. Starch storing amyloplasts can also be converted to chromoplasts, and it's possible for proplastids to develop straight into chromoplasts. Chromoplasts and amyloplasts can also become chloroplasts, like what happens when you illuminate a carrot or a potato. If a plant is injured, or something else causes a plant cell to revert to a meristematic state, chloroplasts and other plastids can turn back into proplastids. Chloroplast, amyloplast, chromoplast, proplast, etc., are not absolute states—intermediate forms are common.127
|This section requires expansion with: functions, Z-ring dynamic assembly, regulators such as Giant Chloroplast 1. (February 2013)|
Most chloroplasts in a photosynthetic cell do not develop directly from proplastids or etioplasts. In fact, a typical shoot meristematic plant cell contains only 7–20 proplastids. These proplastids differentiate into chloroplasts, which divide to create the 30–70 chloroplasts found in a mature photosynthetic plant cell. If the cell divides, chloroplast division provides the additional chloroplasts to partition between the two daughter cells.130
In single-celled algae, chloroplast division is the only way new chloroplasts are formed. There is no proplastid differentiation—when an algal cell divides, its chloroplast divides along with it, and each daughter cell receives a mature chloroplast.129
Almost all chloroplasts in a cell divide, rather than a small group of rapidly dividing chloroplasts.131 Chloroplasts have no definite S-phase—their DNA replication is not synchronized or limited to that of their host cells.132 Much of what we know about chloroplast division comes from studying the alga Cyanidioschyzon merolæ.112
The division process starts when the proteins FtsZ1 and FtsZ2 assemble into filaments, and with the help of a protein ARC6, form a structure called a Z-ring within the chloroplast's stroma.112133 The Min system manages the placement of the Z-ring, ensuring that the chloroplast is cleaved more or less evenly. The protein MinD prevents FtsZ from linking up and forming filaments. Another protein ARC3 may also be involved, but it is not very well understood. These proteins are active at the poles of the chloroplast, preventing Z-ring formation there, but near the center of the chloroplast, MinE inhibits them, allowing the Z-ring to form.112
Next, the two plastid-dividing rings, or PD rings form. The inner plastid-dividing ring is located in the inner side of the chloroplast's inner membrane, and is formed first.112 The outer plastid-dividing ring is found wrapped around the outer chloroplast membrane. It consists of filaments about 5 nanometers across,112 arranged in rows 6.4 nanometers apart, and shrinks to squeeze the chloroplast. This is when chloroplast constriction begins.133
In a few species like Cyanidioschyzon merolæ, chloroplasts have a third plastid-dividing ring located in the chloroplast's intermembrane space.112133
Late into the constriction phase, dynamin proteins assemble around the outer plastid-dividing ring,133 helping provide force to squeeze the chloroplast.112 Meanwhile, the Z-ring and the inner plastid-dividing ring break down.133 During this stage, the many chloroplast DNA plasmids floating around in the stroma are partitioned and distributed to the two forming daughter chloroplasts.134
A remnant of the outer plastid dividing ring remains floating between the two daughter chloroplasts, and a remnant of the dynamin ring remains attached to one of the daughter chloroplasts.133
Of the five or six rings involved in chloroplast division, only the outer plastid-dividing ring is present for the entire constriction and division phase—while the Z-ring forms first, constriction does not begin until the outer plastid-dividing ring forms.133
In species of algae which contain a single chloroplast, regulation of chloroplast division is extremely important to ensure that each daughter cell receives a chloroplast. In organisms like plants, whose cells contain multiple chloroplasts, coordination is looser and less important. It's likely that chloroplast and cell division are somewhat synchronized, though the mechanisms for it are mostly unknown.112
Light has been shown to be a requirement for chloroplast division. Chloroplasts can grow and progress through some of the constriction stages under poor quality green light, but are slow to complete division—they require exposure to bright white light to complete division. Spinach leaves grown under green light have been observed to contain many large dumbbell-shaped chloroplasts. Exposure to white light can stimulate these chloroplasts to divide and reduce the population of dumbbell-shaped chloroplasts.131134
Like mitochondria, chloroplasts are usually inherited from a single parent. Biparental chloroplast inheritance—where plastid genes are inherited from both parent plants—occurs in very low levels in some flowering plants.135
Many mechanisms prevent biparental chloroplast DNA inheritance including selective destruction of chloroplasts or their genes within the gamete or zygote, and chloroplasts from one parent being excluded from the embryo. Parental chloroplasts can be sorted so that only one type is present in each offspring.136
Gymnosperms, such as pine trees, mostly pass on chloroplasts paternally,137 while flowering plants often inherit chloroplasts maternally.138139 Flowering plants were once thought to only inherit chloroplasts maternally. However, there are now many documented cases of angiosperms inheriting chloroplasts paternally.135
Angiosperms which pass on chloroplasts maternally have many ways to prevent paternal inheritance. Most of them produce sperm cells which do not contain any plastids. There are many other documented mechanisms that prevent paternal inheritance in these flowering plants, such as different rates of chloroplast replication within the embryo.135
Among angiosperms, paternal chloroplast inheritance is observed more often in hybrids than in offspring from parents of the same species. This suggests that incompatible hybrid genes might interfere with the mechanisms that prevent paternal inheritance.135
Recently, chloroplasts have caught attention by developers of genetically modified crops. Since in most flowering plants, chloroplasts are not inherited from the male parent, transgenes in these plastids cannot be disseminated by pollen. This makes plastid transformation a valuable tool for the creation and cultivation of genetically modified plants that are biologically contained, thus posing significantly lower environmental risks. This biological containment strategy is therefore suitable for establishing the coexistence of conventional and organic agriculture. While the reliability of this mechanism has not yet been studied for all relevant crop species, recent results in tobacco plants are promising, showing a failed containment rate of transplastomic plants at 3 in 1,000,000.139
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