Structure of a typical higher-plant chloroplast. The greenchlorophyll is contained in stacks of disk-likethylakoids.Chloroplasts, containing thylakoids, visible in the cells ofRosulabryum capillare, a type ofmoss
Chloroplasts are highly dynamic—they circulate and are moved around within cells. Their behavior is strongly influenced by environmental factors like light color and intensity. Chloroplasts cannot be made anew by the plant cell and must be inherited by each daughter cell during cell division, which is thought to be inherited from their ancestor—a photosyntheticcyanobacterium that wasengulfed by an earlyeukaryotic cell.[3]
Chloroplasts evolved from an ancient cyanobacterium that was engulfed by an early eukaryotic cell. Because of their endosymbiotic origins, chloroplasts, likemitochondria, contain their ownDNA separate from thecell nucleus. With one exception (theamoeboidPaulinella chromatophora), all chloroplasts can be traced back to a singleendosymbiotic event. Despite this, chloroplasts can be found in extremely diverse organisms that are not directly related to each other—a consequence of manysecondary and eventertiary endosymbiotic events.
Discovery and etymology
The first definitive description of a chloroplast (Chlorophyllkörnen, "grain of chlorophyll") was given byHugo von Mohl in 1837 as discrete bodies within the green plant cell.[4] In 1883,Andreas Franz Wilhelm Schimper named these bodies as "chloroplastids" (Chloroplastiden).[5] In 1884,Eduard Strasburger adopted the term "chloroplasts" (Chloroplasten).[6][7][8]
The wordchloroplast is derived from theGreek wordschloros (χλωρός), which means green, andplastes (πλάστης), which means "the one who forms".[9]
Primary endosymbiosis A eukaryote withmitochondria engulfed acyanobacterium in an event ofserial primary endosymbiosis, creating alineage of cells with both organelles.[17]
Approximately twobillion years ago,[18][19][20] a free-livingcyanobacterium entered an earlyeukaryotic cell, either as food or as an internalparasite,[17] but managed to escape thephagocytic vacuole it was contained in and persist inside the cell.[12] This event is calledendosymbiosis, or "cell living inside another cell with a mutual benefit for both". The external cell is commonly referred to as thehost while the internal cell is called theendosymbiont.[17] The engulfed cyanobacteria provided an advantage to the host by providing sugar from photosynthesis.[17] Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to thenucleus of the host.[21] Some of the cyanobacterial proteins were then synthesized by host cell and imported back into the chloroplast (formerly the cyanobacterium), allowing the host to control the chloroplast.[21][22]
Chloroplasts which can be traced back directly to a cyanobacterial ancestor (i.e. without a subsequent endosymbiotic event) are known asprimary plastids ("plastid" in this context means almost the same thing as chloroplast[17]).[23] Chloroplasts that can be traced back to another photosynthetic eukaryotic endosymbiont are calledsecondary plastids ortertiary plastids (discussed below).
Whether primary chloroplasts came from a single endosymbiotic event or multiple independent engulfments across various eukaryotic lineages was long debated. It is now generally held that with one exception (the amoeboidPaulinella chromatophora), chloroplasts arose from a single endosymbiotic event around twobillion years ago and these chloroplasts all sharea single ancestor.[19] It has been proposed this the closest living relative of the ancestral engulfed cyanobacterium isGloeomargarita lithophora.[24][25][26] Separately, somewhere about 90–140 million years ago, this process happened again in theamoeboidPaulinella with a cyanobacterium in the genusProchlorococcus. This independently evolved chloroplast is often called achromatophore instead of a chloroplast.[27][Note 1]
Chloroplasts are believed to have arisen aftermitochondria, since alleukaryotes contain mitochondria, but not all have chloroplasts.[17][28] This is calledserial endosymbiosis—where an early eukaryote engulfed themitochondrion ancestor, and then descendants of it then engulfed the chloroplast ancestor, creating a cell with both chloroplasts and mitochondria.[17]
Secondary and tertiary endosymbiosis
Secondary endosymbiosis consisted of aeukaryoticalga being engulfed by another eukaryote, forming a chloroplast with three or four membranes.
Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga with a primary chloroplast. These chloroplasts are known assecondary plastids.[23]
As a result of the secondary endosymbiotic event, secondary chloroplasts have additional membranes outside of the original two in primary chloroplasts.[29] In secondary plastids, typically only the chloroplast, and sometimes itscell membrane andnucleus remain, forming a chloroplast with three or four membranes[30]—the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and thephagosomal vacuole from the host's cell membrane.[29]
The genes in the phagocytosed eukaryote's nucleus are often transferred to the secondary host's nucleus.[29]Cryptomonads andchlorarachniophytes retain the phagocytosed eukaryote's nucleus, an object called anucleomorph,[29] located between the second and third membranes of the chloroplast.[12][22]
All secondary chloroplasts come fromgreen andred algae. No secondary chloroplasts fromglaucophytes have been observed, probably because glaucophytes are relatively rare in nature, making them less likely to have been taken up by another eukaryote.[29]
Still other organisms, including the dinoflagellatesKarlodinium andKarenia, obtained chloroplasts by engulfing an organism with a secondary plastid. These are calledtertiary plastids.[23]
All primary chloroplasts belong to one of four chloroplast lineages—theglaucophyte chloroplast lineage, therhodophyte ("red") chloroplast lineage, and thechloroplastidan ("green") chloroplast lineage, the amoeboidPaulinella chromatophora lineage.[33] The glaucophyte, rhodophyte, and chloroplastidian lineages are all descended from the same ancestral endosymbiotic event and are all within the groupArchaeplastida.[29]
The glaucophyteCyanophora paradoxa with two chloroplasts in the process of dividing.
The glaucophyte chloroplast group is the smallest of the three primary chloroplast lineages as there are only 25 described glaucophyte species.[34] Glaucophytes diverged first before the red and green chloroplast lineages diverged.[35] Because of this, they are sometimes considered intermediates between cyanobacteria and the red and green chloroplasts.[36] This early divergence is supported by bothphylogenetic studies and physical features present in glaucophyte chloroplasts and cyanobacteria, but not the red and green chloroplasts. First, glaucophyte chloroplasts have apeptidoglycan wall, a type of cell wall otherwise only in bacteria (including cyanobacteria).[Note 2] Second, glaucophyte chloroplasts containconcentric unstackedthylakoids which surround acarboxysome – anicosahedral structure that contains the enzymeRuBisCO responsible forcarbon fixation. Third, starch created by the chloroplast is collected outside the chloroplast.[37] Additionally, like cyanobacteria, both glaucophyte and rhodophyte thylakoids are studded with light collecting structures calledphycobilisomes.
The rhodophyte, orred algae, group is a large and diverse lineage.[29] Rhodophyte chloroplasts are also calledrhodoplasts,[23] literally "red chloroplasts".[38] Rhodoplasts have a double membrane with an intermembrane space andphycobilin pigments organized intophycobilisomes on the thylakoid membranes, preventing their thylakoids from stacking.[12] Some containpyrenoids.[23] Rhodoplasts havechlorophylla and phycobilins[32] for photosynthetic pigments; the phycobilinphycoerythrin is responsible for giving many red algae their distinctivered color.[39] However, since they also contain the blue-greenchlorophylla and other pigments, many are reddish to purple from the combination.[23][dubious –discuss] The red phycoerytherin pigment is an adaptation to help red algae catch more sunlight in deep water[23]—as such, some red algae that live in shallow water have less phycoerythrin in their rhodoplasts, and can appear more greenish.[39] Rhodoplasts synthesize a form of starch calledfloridean starch,[23] which collects into granules outside the rhodoplast, in the cytoplasm of the red alga.[12]
Most green chloroplasts aregreen in color, though some aren't due to accessory pigments that override the green from chlorophylls, such as in the resting cells ofHaematococcus pluvialis. Green chloroplasts differ from glaucophyte and red algal chloroplasts in that they have lost theirphycobilisomes, and containchlorophyllb.[12] They have also lost thepeptidoglycan wall between their double membrane, leaving an intermembrane space.[12] Someplants have kept somegenes required the synthesis of peptidoglycan, but have repurposed them for use inchloroplast division instead.[41] Chloroplastida lineages also keep theirstarchinside their chloroplasts.[12][32][40] In plants and some algae, the chloroplast thylakoids are arranged in grana stacks. Some green algal chloroplasts, as well as those ofhornworts, contain a structure called apyrenoid,[12] that concentrateRuBisCO and CO2 in the chloroplast, functionally similar to the glaucophytecarboxysome.[42][43]
There are some lineages of non-photosynthetic parasitic green algae that have lost their chloroplasts entirely, such asPrototheca,[32] or have no chloroplast while retaining the separate chloroplast genome, as inHelicosporidium.[44] Morphological and physiological similarities, as well asphylogenetics, confirm that these are lineages that ancestrally had chloroplasts but have since lost them.[44][45]
Light micrograph of the amoeboidPaulinella chromatophora
The photosynthetic amoeboids in the genusPaulinella—P. chromatophora, P. micropora, and marineP. longichromatophora—have the only known independently evolved chloroplast, often called achromatophore.[Note 1] While all other chloroplasts originate from a single ancient endosymbiotic event,Paulinella independently acquired an endosymbiotic cyanobacterium from the genusSynechococcus around 90 – 140 million years ago.[27][29] EachPaulinella cell contains one or two sausage-shaped chloroplasts;[21][46] they were first described in 1894 by German biologist Robert Lauterborn.[47]
The chromatophore is highly reduced compared to its free-living cyanobacterial relatives and has limited functions. For example, it has a genome of about 1 millionbase pairs, one third the size ofSynechococcus genomes, and only encodes around 850 proteins.[21] However, this is still much larger than other chloroplast genomes, which are typically around 150,000 base pairs. Chromatophores have also transferred much less of their DNA to the nucleus of their hosts. About 0.3–0.8% of the nuclear DNA inPaulinella is from the chromatophore, compared with 11–14% from the chloroplast in plants.[46] Similar to other chloroplasts,Paulinella provides specific proteins to the chromatophore using a specific targeting sequence.[48] Because chromatophores are much younger compared to the canoncial chloroplasts,Paulinella chromatophora is studied to understand how early chloroplasts evolved.[21]
Secondary and tertiary chloroplast lineages
Green algal derived chloroplasts
Green algae have been taken up by many groups in three or four separate events.[49] Primarily, secondary chloroplasts derived from green algae are in theeuglenids andchlorarachniophytes. They are also found in one lineage ofdinoflagellates[32] and possibly the ancestor of the CASH lineage (cryptomonads,alveolates,stramenopiles andhaptophytes)[50] Many green algal derived chloroplasts containpyrenoids, but unlike chloroplasts in their green algal ancestors, storage product collects in granules outside the chloroplast.[12]
The euglenophytes are a group of commonflagellatedprotists that contain chloroplasts derived from a green alga.[29] Euglenophytes are the only group outsideDiaphoretickes that have chloroplasts without performingkleptoplasty.[51][52] Euglenophyte chloroplasts have three membranes. It is thought that the membrane of the primary endosymbiont host was lost (e.g. the green algal membrane), leaving the two cyanobacterial membranes and the secondary host's phagosomal membrane.[29] Euglenophyte chloroplasts have apyrenoid andthylakoids stacked in groups of three. The carbon fixed through photosynthesis is stored in the form ofparamylon, which is contained in membrane-bound granules in the cytoplasm of the euglenophyte.[12][32]
Chlorarachniophytes are a rare group of organisms that also contain chloroplasts derived from green algae,[29] though their story is more complicated than that of the euglenophytes. The ancestor of chlorarachniophytes is thought to have been a eukaryote with ared algal derived chloroplast. It is then thought to have lost its first red algal chloroplast, and later engulfed a green alga, giving it its second, green algal derived chloroplast.[32]
Chlorarachniophyte chloroplasts are bounded by four membranes, except near the cell membrane, where the chloroplast membranes fuse into a double membrane.[12] Their thylakoids are arranged in loose stacks of three.[12] Chlorarachniophytes have a form of polysaccharide calledchrysolaminarin, which they store in the cytoplasm,[32] often collected around the chloroplastpyrenoid, which bulges into the cytoplasm.[12]
Chlorarachniophyte chloroplasts are notable because the green alga they are derived from has not been completely broken down—its nucleus still persists as anucleomorph[29] found between the second and third chloroplast membranes[12]—theperiplastid space, which corresponds to the green alga's cytoplasm.[32]
Lepidodinium chlorophorum's green colour is caused by a plastid derived fromPedinophyceae.
Dinoflagellates in the genusLepidodinium have lost their original peridinin chloroplast and replaced it with a green algal derived chloroplast (more specifically, aprasinophyte).[12][53]Lepidodinium is the only dinoflagellate that has a chloroplast that's not from therhodoplast lineage. The chloroplast is surrounded by two membranes and has no nucleomorph—all the nucleomorph genes have been transferred to the dinophytenucleus.[53] The endosymbiotic event that led to this chloroplast was serial secondary endosymbiosis rather than tertiary endosymbiosis—the endosymbiont was agreen alga containing a primary chloroplast (making a secondary chloroplast).[32]
Tripartite symbiosis
Pseudoblepharisma tenue with its two photosynthetic symbionts.
TheciliatePseudoblepharisma tenue has two bacterial symbionts, one pink, one green. In 2021, both symbionts were confirmed to be photosynthetic: Ca.Thiodictyon intracellulare (Chromatiaceae), apurple sulfur bacterium with a genome just half the size of their closest known relatives; andChlorella sp. K10, a green alga.[54] There is also a variant ofPseudoblepharisma tenue that only contains chloroplasts from green algae and no endosymbiotic purple bacteria.[55]
Red algal derived chloroplasts
Secondary chloroplasts derived fromred algae appear to have only been taken up only once, which then diversified into a large group calledchromists or chromalveolates. Today they are found in thehaptophytes,cryptomonads,heterokonts,dinoflagellates andapicomplexans (the CASH lineage).[32] Red algal secondary chloroplasts usually contain chlorophyll c and are surrounded by four membranes.[12]
However, chromistmonophyly has been rejected, and it is considered more likely that some chromists acquired their plastids by incorporating another chromist instead of inheriting them from a common ancestor.Cryptophytes seem to have acquired plastids from red algae, which were then transmitted from them to both theHeterokontophytes and theHaptophytes, and then from these last to theMyzozoa.[56]
Cryptophytes, or cryptomonads, are a group of algae that contain a red-algal derived chloroplast. Cryptophyte chloroplasts contain anucleomorph that superficially resembles that of thechlorarachniophytes.[29] Cryptophyte chloroplasts have four membranes. The outermost membrane is continuous with therough endoplasmic reticulum. They synthesize ordinarystarch, which is stored in granules found in the periplastid space—outside the original double membrane, in the place that corresponds to the ancestral red alga's cytoplasm. Inside cryptophyte chloroplasts is apyrenoid andthylakoids in stacks of two.[12] Cryptophyte chloroplasts do not havephycobilisomes,[12] but they do havephycobilin pigments which they keep in the thylakoid space, rather than anchored on the outside of their thylakoid membranes.[12][29]
Cryptophytes may have played a key role in the spreading of red algal based chloroplasts.[57][58]
Haptophytes are similar and closely related to cryptophytes or heterokontophytes.[32] Their chloroplasts lack a nucleomorph,[12][29] their thylakoids are in stacks of three, and they synthesizechrysolaminarin sugar, which are stored in granules completely outside of the chloroplast, in the cytoplasm of the haptophyte.[12]
Heterokont chloroplasts are very similar to haptophyte chloroplasts. They have apyrenoid, triplet thylakoids, and, with some exceptions,[12] four layer plastidic envelope with the outermost membrane connected to theendoplasmic reticulum. Like haptophytes, stramenopiles store sugar inchrysolaminarin granules in the cytoplasm.[12] Stramenopile chloroplasts containchlorophylla and, with a few exceptions,[12]chlorophyllc.[29] They also havecarotenoids which give them their many colors.[39]
The alveolates are a major clade of unicellular eukaryotes of bothautotrophic andheterotrophic members. Many members contain a red-algal derived plastid. One notable characteristic of this diverse group is the frequent loss of photosynthesis. However, a majority of these heterotrophs continue to process a non-photosynthetic plastid.[59]
Apicomplexans
Diagram of Plasmodium, including its apicoplast.
Apicomplexans are a group of alveolates. Like thehelicosproidia, they're parasitic, and have a nonphotosynthetic chloroplast.[32] They were once thought to be related to the helicosproidia, but it is now known that the helicosproida are green algae rather than part of the CASH lineage.[32] The apicomplexans includePlasmodium, themalaria parasite. Many apicomplexans keep avestigial red algal derived chloroplast[60][32] called anapicoplast, which they inherited from their ancestors. 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 theendoplasmic reticulum.[12] Other apicomplexans likeCryptosporidium have lost the chloroplast completely.[60] Apicomplexans store their energy inamylopectin granules that are located in their cytoplasm, even though they are nonphotosynthetic.[12]
The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other thanphotosynthesis.Plant chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesizefatty acids,isopentenyl pyrophosphate,iron-sulfur clusters, and carry out part of theheme pathway.[60] The most important apicoplast function isisopentenyl 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.[60]
Thechromerids are a group of algae known from Australian corals which comprise some close photosynthetic relatives of the apicomplexans. The first member,Chromera velia, was discovered and first isolated in 2001. The discovery ofChromera velia with similar structure to the apicomplexans, provides an important link in the evolutionary history of the apicomplexans and dinophytes. Their plastids have four membranes, lack chlorophyll c and use the type II form ofRuBisCO obtained from a horizontal transfer event.[61]
Thedinoflagellates are yet another very large and diverse group, around half of which are at least partially photosynthetic (i.e.mixotrophic).[39][53] Dinoflagellate chloroplasts have relatively complex history. Most dinoflagellate chloroplasts are secondaryred algal derived chloroplasts. Many dinoflagellates have lost the chloroplast (becoming nonphotosynthetic), some of these have replaced it thoughtertiary endosymbiosis.[63] Others replaced their original chloroplast with agreen algal derived chloroplast.[29][32][53] The peridinin chloroplast is thought to be the dinophytes' "original" chloroplast,[53] which has been lost, reduced, replaced, or has company in several other dinophyte lineages.[32]
The most common dinophyte chloroplast is theperidinin-type chloroplast, characterized by thecarotenoid pigmentperidinin in their chloroplasts, along withchlorophylla andchlorophyllc2.[29][53] Peridinin is not found in any other group of chloroplasts.[53] The peridinin chloroplast is bounded by three membranes (occasionally two),[12] having lost the red algal endosymbiont's original cell membrane.[29][32] The outermost membrane is not connected to the endoplasmic reticulum.[12][53] They contain apyrenoid, and have triplet-stacked thylakoids. Starch is found outside the chloroplast.[12] Peridinin chloroplasts also have DNA that is highlyreduced and fragmented into many small circles.[53] Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast.
Thefucoxanthin dinophyte lineages (includingKarlodinium andKarenia)[32] lost their original red algal derived chloroplast, and replaced it with a new chloroplast derived from ahaptophyte endosymbiont, making these tertiary plastids.Karlodinium andKarenia probably took up different endosymbionts.[32] Because the haptophyte chloroplast has four membranes, tertiary endosymbiosis would be expected to create a six membraned chloroplast, adding the haptophyte'scell membrane and the dinophyte'sphagosomal vacuole.[64] 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.[32][64]
Durinskia is a genus significant to the study of endosymbiotic events and organelle integration.[65]
Some dinophytes, likeKryptoperidinium andDurinskia,[32] have adiatom (heterokontophyte)-derived chloroplast.[29] These chloroplasts are bounded by up tofive membranes,[29] (depending on whether the entire diatom endosymbiont is counted as the chloroplast, or just the red algal derived chloroplast inside it). The diatom endosymbiont has been reduced relatively little—it still retains its originalmitochondria,[32] and hasendoplasmic reticulum,ribosomes, anucleus, and of course, red algal derived chloroplasts—practically a completecell,[66] all inside the host'sendoplasmic reticulum lumen.[32] However the diatom endosymbiont can't store its own food—its storage polysaccharide is found in granules in the dinophyte host's cytoplasm instead.[12][66] The diatom endosymbiont's nucleus is present, but it probably can't be called anucleomorph because it shows no sign ofgenome reduction, and might have even beenexpanded.[32] Diatoms have been engulfed by dinoflagellates at least three times.[32]
The diatom endosymbiont is bounded by a single membrane,[53] inside it are chloroplasts with four membranes. Like the diatom endosymbiont's diatom ancestor, the chloroplasts have triplet thylakoids andpyrenoids.[66]
In some of thesegenera, the diatom endosymbiont's chloroplasts aren't the only chloroplasts in the dinophyte. The original three-membraned peridinin chloroplast is still around, converted to aneyespot.[29][32]
Members of the genusDinophysis have aphycobilin-containing[64] chloroplast taken from acryptophyte.[29] However, the cryptophyte is not an endosymbiont—only the chloroplast seems to have been taken, and the chloroplast has been stripped of itsnucleomorph and outermost two membranes, leaving just a two-membraned chloroplast. Cryptophyte chloroplasts require their nucleomorph to maintain themselves, andDinophysis species grown incell culture alone cannot survive, so it is possible (but not confirmed) that theDinophysis chloroplast is akleptoplast—if so,Dinophysis chloroplasts wear out andDinophysis species must continually engulf cryptophytes to obtain new chloroplasts to replace the old ones.[53]
Chloroplasts, like other endosymbiotic organelles, contain agenome separate from that in the cellnucleus. The existence ofchloroplast DNA (cpDNA) was identified biochemically in 1959,[69] and confirmed by electron microscopy in 1962.[70] The discoveries that the chloroplast contains ribosomes[71] and performs protein synthesis[72] revealed that the chloroplast is genetically semi-autonomous. Chloroplast DNA was first sequenced in 1986.[73] Since then, hundreds of chloroplast genomes from various species have beensequenced, but they are mostly those ofland plants andgreen algae—glaucophytes,red algae, and other algal groups are extremely underrepresented, potentially introducing somebias in views of "typical" chloroplast DNA structure and content.[74]
Chloroplast DNA Interactive gene map of chloroplast DNA fromNicotiana tabacum. Segments with labels on the inside are on the B strand ofDNA, segments with labels on the outside are on the A strand. Notches indicateintrons.
Molecular structure
With few exceptions, most chloroplasts have their entire chloroplast genome combined into a single large circular DNA molecule,[74] typically 120,000–170,000base pairs long[75][76][77][18] and a mass of about 80–130 milliondaltons.[78] While chloroplast genomes can almost always be assembled into a circular map, the physical DNA molecules inside cells take on a variety of linear and branching forms.[74][79] New chloroplasts may contain up to 100 copies of their genome,[75] though the number of copies decreases to about 15–20 as the chloroplasts age.[80]
Chloroplast DNA is usually condensed intonucleoids, which can contain multiple copies of the chloroplast genome. Many nucleoids can be found in each chloroplast.[78] In primitivered algae, the chloroplast DNA nucleoids are clustered in the center of the chloroplast, while in green plants andgreen algae, the nucleoids are dispersed throughout thestroma.[81] Chloroplast DNA is not associated with truehistones, proteins that are used to pack DNA molecules tightly in eukaryote nuclei.[17] Though inred algae, similar proteins tightly pack each chloroplast DNA ring in anucleoid.[81]
Many chloroplast genomes contain twoinverted repeats, which separate a long single copy section (LSC) from a short single copy section (SSC).[77] A given pair of inverted repeats are rarely identical, but they are always very similar to each other, apparently resulting fromconcerted evolution.[74] The inverted repeats vary wildly in length, ranging from 4,000 to 25,000base pairs long each and containing as few as four or as many as over 150 genes.[74] The inverted repeat regions are highlyconserved in land plants, and accumulate few mutations.[77][82]
Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages (glaucophyta andrhodophyceae), suggesting that they predate the chloroplast.[74] Some chloroplast genomes have since lost[82][83] or flipped the inverted repeats (making themdirect repeats).[74] It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast genomes which have lost some of the inverted repeat segments tend to get rearranged more.[83]
Chloroplast DNA replication via multipleD-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 viaelectron microscopy since the 1970s.[86][87] 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 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.[86][88] Transcription starts at specific points of origin. Multiple replication forks open up, allowing replication machinery to transcribe 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 ofdeamination seen in cpDNA.[86] Deamination occurs when an amino group is lost and is a mutation that often results in base changes. When adenine is deaminated, it becomeshypoxanthine. Hypoxanthine can bind to cytosine, and when the XC base pair is replicated, it becomes a GC (thus, an A → G base change).[89]
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).[86] 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.[86][88]
One of competing model for cpDNA replication asserts that most cpDNA is linear and participates inhomologous recombination and replication structures similar to the linear and circular DNA structures ofbacteriophage T4.[88][90] It has been established that some plants have linear cpDNA, such as maize, and that more species still contain complex structures that scientists do not yet understand.[88] When the original experiments on cpDNA were performed, scientists did notice linear structures; however, they attributed these linear forms to broken circles.[88] 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.[88] At the same time, homologous recombination does not expand the multiple A --> G gradients seen in plastomes.[86] Because of the failure to explain the deamination gradient as well as the numerous plant species that have been shown to have circular cpDNA, the predominant theory continues to hold that most cpDNA is circular and most likely replicates via a D loop mechanism.
Gene content and protein synthesis
The ancestral cyanobacteria that led to chloroplasts probably had a genome that contained over 3000 genes, but only approximately 100 genes remain in contemporary chloroplast genomes.[18][22][76] These genes code for a variety of things, mostly to do with theprotein pipeline andphotosynthesis. As inprokaryotes, genes in chloroplast DNA are organized intooperons.[22] Unlikeprokaryotic DNA molecules, chloroplast DNA molecules containintrons (plantmitochondrial DNAs do too, but not human mtDNAs).[91]
Among land plants, the contents of the chloroplast genome are fairly similar.[77]
Chloroplast genome reduction and gene transfer
Over time, many parts of the chloroplast genome were transferred to thenuclear genome of the host,[75][76][92] a process calledendosymbiotic gene transfer. As a result, the chloroplast genome is heavilyreduced compared to that of free-living cyanobacteria. Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more than 1500 genes in their genome.[93] Recently, a plastid without a genome was found, demonstrating chloroplasts can lose their genome during endosymbiotic the gene transfer process.[94]
Endosymbiotic gene transfer is how we know about thelost chloroplasts in many CASH lineages. Even if a chloroplast is eventually lost, the genes it donated to the former host's nucleus persist, providing evidence for the lost chloroplast's existence. For example, whilediatoms (aheterokontophyte) now have ared algal derived chloroplast, the presence of manygreen algal genes in the diatom nucleus provide evidence that the diatom ancestor had agreen algal derived chloroplast at some point, which was subsequently replaced by the red chloroplast.[50]
In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast,[46] up to 18% inArabidopsis, corresponding to about 4,500 protein-coding genes.[95] There have been a few recent transfers of genes from the chloroplast DNA to the nuclear genome in land plants.[76]
Of the approximately 3000 proteins found in chloroplasts, some 95% of them are encoded by nuclear genes. Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome. As a result,protein synthesis must be coordinated between the chloroplast and the nucleus. The chloroplast is mostly under nuclear control, though chloroplasts can also give out signals regulatinggene expression in the nucleus, calledretrograde signaling.[96] Recent research indicates that parts of the retrograde signaling network once considered characteristic for land plants emerged already in an algal progenitor,[97][98][99] integrating into co-expressed cohorts of genes in the closest algal relatives of land plants.[100]
Protein synthesis within chloroplasts relies on twoRNA polymerases. One is coded by the chloroplast DNA, the other is ofnuclear origin. The two RNA polymerases may recognize and bind to different kinds ofpromoters within the chloroplast genome.[101] Theribosomes in chloroplasts are similar to bacterial ribosomes.[102]
This sectionneeds expansion with: Genome size differences between algae and land plants, chloroplast stuff coded by the nucleus. You can help bymaking an edit requestadding to it.(January 2013)
Because so many chloroplast genes have been moved to the nucleus, manyproteins that would originally have beentranslated in the chloroplast are now synthesized in the cytoplasm of the plant cell. These proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes.[103]
Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many becameexaptations, taking on new functions like participating incell division,protein routing, and evendisease resistance. A few chloroplast genes found new homes in themitochondrial genome—most became nonfunctionalpseudogenes, though a fewtRNA genes still work in themitochondrion.[93] Some transferred chloroplast DNA protein products get directed to thesecretory pathway,[93] though manysecondary plastids are bounded by an outermost membrane derived from the host'scell membrane, and thereforetopologically outside of the cell because to reach the chloroplast from thecytosol, thecell membrane must be crossed, which signifies entrance into theextracellular space. In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway.[32]
In most, but not all cases, nuclear-encoded chloroplast proteins aretranslated with acleavable transit peptide that's added to the N-terminus of the protein precursor. Sometimes the transit sequence is found on the C-terminus of the protein,[105] or within the functional part of the protein.[103]
Transport proteins and membrane translocons
After a chloroplastpolypeptide is synthesized on aribosome in thecytosol, an enzymespecific to chloroplast proteins[106]phosphorylates, or adds aphosphate group to many (but not all) of them in their transit sequences.[103]Phosphorylation helps many proteins bind the polypeptide, keeping it fromfolding prematurely.[103] This is important because it prevents chloroplast proteins from assuming their active form and carrying out their chloroplast functions in the wrong place—thecytosol.[107][108] At the same time, they have to keep just enough shape so that they can be recognized by the chloroplast.[107] These proteins also help the polypeptide get imported into the chloroplast.[103]
From here, chloroplast proteins bound for the stroma must pass through two protein complexes—theTOC complex, ortranslocon on theouterchloroplast membrane, and theTIC translocon, ortranslocon on theinnerchloroplast membranetranslocon.[103] Chloroplast polypeptide chains probably often travel through the two complexes at the same time, but the TIC complex can also retrieve preproteins lost in theintermembrane space.[103]
Inland plants, chloroplasts are generally lens-shaped, 3–10 μm in diameter and 1–3 μm thick.[109][18] Corn seedling chloroplasts are ≈20 μm3 in volume.[18] Greater diversity in chloroplast shapes exists among thealgae, which often contain a single chloroplast[12] that can be shaped like a net (e.g.,Oedogonium),[110] a cup (e.g.,Chlamydomonas),[111] a ribbon-like spiral around the edges of the cell (e.g.,Spirogyra),[112] or slightly twisted bands at the cell edges (e.g.,Sirogonium).[113] Some algae have two chloroplasts in each cell; they are star-shaped inZygnema,[114] or may follow the shape of half the cell inorderDesmidiales.[115] In some algae, the chloroplast takes up most of the cell, with pockets for thenucleus and other organelles,[12] for example, some species ofChlorella have a cup-shaped chloroplast that occupies much of the cell.[116]
All chloroplasts have at least three membrane systems—the outer chloroplast membrane, the inner chloroplast membrane, and thethylakoid system. The two innermostlipid-bilayer membranes[117] that surround all chloroplasts correspond to the outer and innermembranes of the ancestral cyanobacterium'sgram negative cell wall,[29][118][119] and not thephagosomal membrane from the host, which was probably lost.[29] Chloroplasts that are the product ofsecondary endosymbiosis may have additional membranes surrounding these three.[30] Inside the outer and inner chloroplast membranes is the chloroplaststroma, a semi-gel-like fluid[23] that makes up much of a chloroplast's volume, and in which the thylakoid system floats.
Chloroplast ultrastructure(interactive diagram) Chloroplasts have at least three distinct membrane systems, and a variety of things can be found in theirstroma.
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 endosymbioticcyanobacteria. This is often interpreted as meaning the outer chloroplast membrane is the product of the host'scell membrane infolding to form a vesicle to surround the ancestralcyanobacterium—which is not true—both chloroplast membranes arehomologous to the cyanobacterium's original double membranes.[29]
The chloroplast double membrane is also often compared to themitochondrial double membrane. This is not a valid comparison—the inner mitochondria membrane is used to runproton pumps and carry outoxidative phosphorylation across to generateATP energy. The only chloroplast structure that can be consideredanalogous to it is the internal thylakoid system. Even so, in terms of "in-out", the direction of chloroplastH+ ion flow is in the opposite direction compared to oxidative phosphorylation in mitochondria.[23][120] In addition, in terms of function, the inner chloroplast membrane, which regulates metabolite passage and synthesizes some materials, has no counterpart in the mitochondrion.[23]
The outer chloroplast membrane is a semi-porous membrane that small molecules andions can easily diffuse across.[121] However, it is not permeable to largerproteins, so chloroplastpolypeptides being synthesized in the cellcytoplasm must be transported across the outer chloroplast membrane by theTOC complex, ortranslocon on theouterchloroplast membrane.[103]
The chloroplast membranes sometimes protrude out into the cytoplasm, forming astromule, orstroma-containing tubule. Stromules are very rare in chloroplasts, and are much more common in otherplastids likechromoplasts andamyloplasts in petals and roots, respectively.[122][123] They may exist to increase the chloroplast'ssurface area for cross-membrane transport, because they are often branched and tangled with theendoplasmic reticulum.[124] When they were first observed in 1962, some plant biologists dismissed the structures as artifactual, claiming that stromules were just oddly shaped chloroplasts with constricted regions ordividing chloroplasts.[125] However, there is a growing body of evidence that stromules are functional, integral features of plant cell plastids, not merely artifacts.[126]
Usually, a thin intermembrane space about 10–20nanometers thick exists between the outer and inner chloroplast membranes.[127]
Glaucophyte algal chloroplasts have apeptidoglycan layer between the chloroplast membranes. It corresponds to thepeptidoglycan cell wall of theircyanobacterial ancestors, which is located between their two cell membranes. These chloroplasts are calledmuroplasts (from Latin"mura", meaning "wall"). Other chloroplasts were assumed to have lost the cyanobacterial wall, leaving an intermembrane space between the two chloroplast envelope membranes,[23] but has since been found also in moss, lycophytes and ferns.[128]
The inner chloroplast membrane borders the stroma and regulates passage of materials in and out of the chloroplast. After passing through theTOC complex in the outer chloroplast membrane,polypeptides must pass through theTIC complex(translocon on theinnerchloroplast membrane) which is located in the inner chloroplast membrane.[103]
In addition to regulating the passage of materials, the inner chloroplast membrane is wherefatty acids,lipids, andcarotenoids are synthesized.[23]
Peripheral reticulum
Some chloroplasts contain a structure called thechloroplast peripheral reticulum.[127] It is often found in the chloroplasts ofC4 plants, though it has also been found in some C3angiosperms,[23] and even somegymnosperms.[129] The chloroplast peripheral reticulum consists of a maze of membranous tubes and vesicles continuous with theinner chloroplast membrane that extends into the internalstromal fluid of the chloroplast. Its purpose is thought to be to increase the chloroplast'ssurface area for cross-membrane transport between its stroma and the cellcytoplasm. The small vesicles sometimes observed may serve astransport vesicles to shuttle stuff between thethylakoids and intermembrane space.[130]
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 ofcytoplasmic ribosomes (around 17nm vs 25nm).[127] They takemRNAs transcribed from thechloroplast DNA andtranslate them into protein. While similar tobacterial ribosomes,[17] chloroplast translation is more complex than in bacteria, so chloroplast ribosomes include some chloroplast-unique features.[131][132]
Plastoglobuli (singularplastoglobulus, sometimes spelledplastoglobule(s)), are spherical bubbles oflipids andproteins[23] about 45–60 nanometers across.[137] They are surrounded by alipid monolayer.[137] Plastoglobuli are found in all chloroplasts,[127] but become more common when the chloroplast is underoxidative stress,[137] or when it ages and transitions into agerontoplast.[23] Plastoglobuli also exhibit a greater size variation under these conditions.[137] They are also common inetioplasts, but decrease in number as the etioplasts mature into chloroplasts.[137]
Plastoglobuli were once thought to be free-floating in thestroma, but it is now thought that they are permanently attached either to athylakoid or to another plastoglobulus attached to a thylakoid, a configuration that allows a plastoglobulus to exchange its contents with the thylakoid network.[137] In normal green chloroplasts, the vast majority of plastoglobuli occur singularly, attached directly to their parent thylakoid. In old or stressed chloroplasts, plastoglobuli tend to occur in linked groups or chains, still always anchored to a thylakoid.[137]
Plastoglobuli form when a bubble appears between the layers of thelipid bilayer of the thylakoid membrane, or bud from existing plastoglobuli—though they never detach and float off into the stroma.[137] Practically all plastoglobuli form on or near the highly curved edges of thethylakoid disks or sheets. They are also more common on stromal thylakoids than ongranal ones.[137]
Starch granules are very common in chloroplasts, typically taking up 15% of the organelle's volume,[138] though in some other plastids likeamyloplasts, they can be big enough to distort the shape of the organelle.[127] Starch granules are simply accumulations of starch in the stroma, and are not bounded by a membrane.[127]
Starch granules appear and grow throughout the day, as the chloroplast synthesizessugars, and are consumed at night to fuelrespiration and continue sugar export into thephloem,[139] though in mature chloroplasts, it is rare for a starch granule to be completely consumed or for a new granule to accumulate.[138]
Starch granules vary in composition and location across different chloroplast lineages. Inred algae, starch granules are found in thecytoplasm rather than in the chloroplast.[140] InC4 plants,mesophyll chloroplasts, which do not synthesize sugars, lack starch granules.[23]
The chloroplast stroma contains many proteins, though the most common and important isRuBisCO, which is probably also the most abundant protein on the planet.[120]RuBisCO is the enzyme that fixesCO2 into sugar molecules. InC3 plants, RuBisCO is abundant in all chloroplasts, though inC4 plants, it is confined to thebundle sheath chloroplasts, where theCalvin cycle is carried out in C4 plants.[141]
The chloroplasts of somehornworts[142] and algae contain structures calledpyrenoids. They are not found in higher plants.[143] Pyrenoids are roughly spherical and highly refractive bodies which are a site of starch accumulation in plants that contain them. They consist of a matrix opaque to electrons, surrounded by two hemispherical starch plates. The starch is accumulated as the pyrenoids mature.[144] In algae withcarbon concentrating mechanisms, the enzymeRuBisCO is found in the pyrenoids. Starch can also accumulate around the pyrenoids when CO2 is scarce.[143] Pyrenoids can divide to form new pyrenoids, or be produced"de novo".[144][145]
Scanning transmission electron microscope imaging of a chloroplast (Top) 10-nm-thick STEM tomographic slice of a lettuce chloroplast. Grana stacks are interconnected by unstacked stromal thylakoids, called "stroma lamellae". Round inclusions associated with the thylakoids are plastoglobules. Scalebar=200 nm. See.[146] (Bottom) Large-scale 3D model generated from segmentation of tomographic reconstructions by STEM. grana=yellow; stroma lamellae=green; plastoglobules=purple; chloroplast envelope=blue. See.[146]
Thylakoids (sometimes spelledthylakoïds),[147] are small interconnected sacks which contain the membranes that thelight reactions of photosynthesis take place on. The wordthylakoid comes from the Greek wordthylakos which means "sack".[148]
Granum-stroma assembly structure The prevailing model of the granum-stroma assembly is stacks of granal thylakoids wrapped by right-handed helical stromal thylakoids which are connected to large parallel sheets of stromal thylakoids and adjacent right-handed helices by left-handed helical structures. (Based on[146]).
Using alight microscope, it is just barely possible to see tiny green granules—which were namedgrana.[127] Withelectron microscopy, it became possible to see the thylakoid system in more detail, revealing it to consist of stacks of flatthylakoids which made up the grana, and long interconnecting stromal thylakoids which linked different grana.[127]In thetransmission electron microscope, thylakoid membranes appear as alternating light-and-dark bands, 8.5 nanometers thick.[127]
The three-dimensional structure of the thylakoid membrane system has been disputed. Many models have been proposed, the most prevalent being thehelical model, in which granum stacks of thylakoids are wrapped by helical stromal thylakoids.[150] Another model known as the 'bifurcation model', which was based on the first electron tomography study of plant thylakoid membranes, depicts the stromal membranes as wide lamellar sheets perpendicular to the grana columns which bifurcates into multiple parallel discs forming the granum-stroma assembly.[151] The helical model was supported by several additional works,[149][152] but ultimately it was determined in 2019 that features from both the helical and bifurcation models are consolidated by newly discovered left-handed helical membrane junctions.[146] Likely for ease, the thylakoid system is still commonly depicted by older "hub and spoke" models where the grana are connected to each other by tubes of stromal thylakoids.[153]
Grana consist of a stacks of flattened circular granal thylakoids that resemble pancakes. Each granum can contain anywhere from two to a hundred thylakoids,[127] though grana with 10–20 thylakoids are most common.[149] Wrapped around the grana are multiple parallel right-handed helical stromal thylakoids, also known as frets or lamellar thylakoids. The helices ascend at an angle of ~20°, connecting to each granal thylakoid at a bridge-like slit junction.[149][152][146]
The stroma lamellae extend as large sheets perpendicular to the grana columns. These sheets are connected to the right-handed helices either directly or through bifurcations that form left-handed helical membrane surfaces.[146] The left-handed helical surfaces have a similar tilt angle to the right-handed helices (~20°), but ¼ the pitch. Approximately 4 left-handed helical junctions are present per granum, resulting in a pitch-balanced array of right- and left-handed helical membrane surfaces of different radii and pitch that consolidate the network with minimal surface and bending energies.[146] 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.[149]
There are two types of thylakoids—granal thylakoids, which are arranged in grana, and stromal thylakoids, which are in contact with thestroma. Granal thylakoids are pancake-shaped circular disks about 300–600 nanometers in diameter. Stromal thylakoids arehelicoid sheets that spiral around grana.[149] The flat tops and bottoms of granal thylakoids contain only the relatively flatphotosystem II protein complex. This allows them to stack tightly, forming grana with many layers of tightly appressed membrane, called granal membrane, increasing stability andsurface area for light capture.[149]
In contrast,photosystem I andATP 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.[149]
The number of thylakoids and the total thylakoid area of a chloroplast is influenced by light exposure. Shaded chloroplasts contain larger and moregrana 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.[130]
Pigments and chloroplast colors
Inside the photosystems embedded in chloroplast thylakoid membranes are variousphotosynthetic pigments, which absorb and transferlight energy. The types of pigments found are different in various groups of chloroplasts, and are responsible for a wide variety of chloroplast colorations. Otherplastid types, such as theleucoplast and thechromoplast, contain little chlorophyll and do not carry out photosynthesis.
Chlorophyllc is mainly found in secondary endosymbiotic chloroplasts that originated from ared alga, although it is not found in chloroplasts of red algae themselves. Chlorophyllc is also found in somegreen algae andcyanobacteria.[12]
Chlorophyllsd andf are pigments found only in some cyanobacteria.[12][155]
In addition to chlorophylls, another group ofyellow–orange[154] pigments calledcarotenoids are also found in the photosystems. There are about thirty photosynthetic carotenoids.[156] They help transfer and dissipate excess energy,[12] and their bright colors sometimes override the chlorophyll green, like during thefall, when the leaves ofsome land plants change color.[157]β-carotene is a bright red-orange carotenoid found in nearly all chloroplasts, likechlorophylla.[12]Xanthophylls, especially the orange-redzeaxanthin, are also common.[156] Many other forms of carotenoids exist that are only found in certain groups of chloroplasts.[12]
Phycobilins
Phycobilins are a third group of pigments found incyanobacteria, andglaucophyte,red algal, andcryptophyte chloroplasts.[12][158] Phycobilins come in all colors, thoughphycoerytherin is one of the pigments that makes many red algae red.[159] Phycobilins often organize into relatively large protein complexes about 40 nanometers across calledphycobilisomes.[12] Likephotosystem I andATP synthase, phycobilisomes jut into the stroma, preventing thylakoid stacking in red algal chloroplasts.[12]Cryptophyte chloroplasts and some cyanobacteria don't have their phycobilin pigments organized into phycobilisomes, and keep them in their thylakoid space instead.[12]
Photosynthetic pigments. Presence of pigments across chloroplast groups and cyanobacteria.
To fixcarbon dioxide into sugar molecules in the process ofphotosynthesis, chloroplasts use an enzyme calledRuBisCO. RuBisCO has trouble distinguishing betweencarbon dioxide andoxygen, so at high oxygen concentrations, RuBisCO starts accidentally adding oxygen to sugar precursors. This has the result ofATP energy being wasted and CO2 being released, all with no sugar being produced. This is a big problem, since O2 is produced by the initiallight reactions of photosynthesis, causing issues down the line in theCalvin cycle which uses RuBisCO.[160]
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 inATP andNADPH, are done in themesophyll cells of a C4 leaf. The Calvin cycle, which uses the stored energy to make sugar using RuBisCO, is done in thebundle sheath cells, a layer of cells surrounding avein in aleaf.[160]
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 lackRuBisCO, and have normalgrana andthylakoids,[141] 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 calledC4 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.[160] Because of this, they lack thylakoids organized intograna stacks—though bundle sheath chloroplasts still have free-floating thylakoids in the stroma where they still carry outcyclic electron flow, a light-driven method of synthesizingATP to power the Calvin cycle without generating oxygen. They lackphotosystem II, and only havephotosystem I—the only protein complex needed for cyclic electron flow.[141][160] Because the job of bundle sheath chloroplasts is to carry out the Calvin cycle and make sugar, they often contain largestarch grains.[141]
Both types of chloroplast contain large amounts ofchloroplast peripheral reticulum,[141] which they use to get moresurface area to transport stuff in and out of them.[129][130] Mesophyll chloroplasts have a little more peripheral reticulum than bundle sheath chloroplasts.[161]
Function and chemistry
Guard cell chloroplasts
This sectionneeds expansion with: determined functions, controversial functions, characteristics and population. You can help bymaking an edit requestadding to it.(August 2013)
Unlike most epidermal cells, theguard cells of plantstomata contain relatively well-developed chloroplasts.[162] However, exactly what they do is controversial.[163]
Plants have two main immune responses—thehypersensitive response, in which infected cells seal themselves off and undergoprogrammed cell death, andsystemic 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, producingreactive oxygen species. High levels of reactive oxygen species will cause thehypersensitive response. The reactive oxygen species also directly kill any pathogens within the cell. Lower levels of reactive oxygen species initiatesystemic acquired resistance, triggering defense-molecule production in the rest of the plant.[164]
In some plants, chloroplasts are known to move closer to the infection site and thenucleus during an infection.[164]
Chloroplasts can serve as cellular sensors. After detecting stress in a cell, which might be due to a pathogen, chloroplasts begin producing molecules likesalicylic acid,jasmonic acid,nitric oxide andreactive 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 initiateretrograde signaling—signals from the chloroplast that regulategene expression in the nucleus.[164]
In addition to defense signaling, chloroplasts, with the help of theperoxisomes,[165] help synthesize an important defense molecule,jasmonate. Chloroplasts synthesize all thefatty acids in a plant cell[164][166]—linoleic acid, a fatty acid, is a precursor to jasmonate.[164]
The light reactions take place on the thylakoid membranes. They takelight energy and store it inNADPH, a form of NADP+, andATP to fuel thedark reactions.
ATP is the phosphorylated version ofadenosine 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 getsreduced, meaning it picks up electrons, becomingNADPH.
Like mitochondria, chloroplasts use thepotential energy stored in anH+, or hydrogen ion, gradient to generate ATP energy. The twophotosystems capture light energy to energizeelectrons taken fromwater, and release them down anelectron transport chain. Themolecules between the photosystems harness the electrons' energy to pump hydrogen ions into the thylakoid space, creating aconcentration gradient, with more hydrogen ions (up to a thousand times as many)[120] inside the thylakoid system than in the stroma. The hydrogen ions in the thylakoid space thendiffuse back down their concentration gradient, flowing back out into the stroma throughATP synthase. ATP synthase uses the energy from the flowing hydrogen ions tophosphorylateadenosine diphosphate intoadenosine triphosphate, or ATP.[120][169] Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there, in position to be used in the dark reactions.[170]
Because NADP+ reduction removes electrons from the electron transport chains, they must be replaced—the job ofphotosystem II, which splitswater molecules (H2O) to obtain the electrons from itshydrogen atoms.[120][167]
Whilephotosystem IIphotolyzes 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 termedcyclic photophosphorylation because the electrons are recycled. Cyclic photophosphorylation is common inC4 plants, which need moreATP thanNADPH.[160]
The Calvin cycle(Interactive diagram) TheCalvin cycle incorporates carbon dioxide into sugar molecules.
TheCalvin cycle, also known as thedark reactions, is a series of biochemical reactions that fixesCO2 intoG3P sugar molecules and uses the energy and electrons from theATP andNADPH made in the light reactions. The Calvin cycle takes place in the stroma of the chloroplast.[160]
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.[11]
Carbon fixation and G3P synthesis
The Calvin cycle starts by using the enzymeRuBisCO to fix CO2 into five-carbonRibulose bisphosphate (RuBP) molecules. The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called3-phosphoglyceric acid, or 3-PGA.TheATP andNADPH made in the light reactions is used to convert the 3-PGA intoglyceraldehyde-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.[160]
Sugars and starches
Sucrose is made up of aglucose monomer (left), and afructose monomer (right).
Glyceraldehyde-3-phosphate can double up to form larger sugar molecules likeglucose andfructose. These molecules are processed, and from them, the still largersucrose, adisaccharide commonly known as table sugar, is made, though this process takes place outside of the chloroplast, in thecytoplasm.[171]
Alternatively, glucosemonomers in the chloroplast can be linked together to makestarch, which accumulates into thestarch grains found in the chloroplast.[171]Under conditions such as high atmospheric CO2 concentrations, these starch grains may grow very large, distorting the grana and thylakoids. The starch granules displace the thylakoids, but leave them intact.[172]Waterloggedroots can also causestarch buildup in the chloroplasts, possibly due to lesssucrose being exported out of the chloroplast (or more accurately, theplant cell). This depletes a plant'sfree phosphate supply, which indirectly stimulates chloroplast starch synthesis.[172]While linked to low photosynthesis rates, the starch grains themselves may not necessarily interfere significantly with the efficiency of photosynthesis,[173] and might simply be a side effect of another photosynthesis-depressing factor.[172]
Photorespiration
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 toRuBP. 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.[167] 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 calledcarbon dioxide concentrating mechanisms, or CCMs. These includeCrassulacean acid metabolism,C4 carbon fixation,[167] andpyrenoids. Chloroplasts in C4 plants are notable as they exhibit a distinctchloroplast dimorphism.
pH
Because of theH+ gradient across the thylakoid membrane, the interior of the thylakoid isacidic, with apH around 4,[174] while the stroma is slightly basic, with a pH of around 8.[175]The optimal stroma pH for the Calvin cycle is 8.1, with the reaction nearly stopping when the pH falls below 7.3.[176]
CO2 in water can formcarbonic acid, which can disturb the pH of isolated chloroplasts, interfering with photosynthesis, even though CO2 isused in photosynthesis. However, chloroplasts in livingplant cells are not affected by this as much.[175]
Chloroplasts can pumpK+ and H+ ions in and out of themselves using a poorly understood light-driven transport system.[175]
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.[176]
Amino acid synthesis
Chloroplasts alone make almost all of a plant cell'samino acids in theirstroma[177] except thesulfur-containing ones likecysteine andmethionine.[178][179] Cysteine is made in the chloroplast (theproplastid too) but it is also synthesized in thecytosol andmitochondria, probably because it has trouble crossing membranes to get to where it is needed.[179] The chloroplast is known to make the precursors to methionine but it is unclear whether the organelle carries out the last leg of the pathway or if it happens in thecytosol.[180]
This sectionneeds expansion with: needs more about lipids, also paramylon. You can help bymaking an edit requestadding to it.(March 2013)
The plastid is the site of diverse and complexlipid synthesis in plants.[181][182] The carbon used to form the majority of the lipid is fromacetyl-CoA, which is the decarboxylation product ofpyruvate.[181] Pyruvate may enter the plastid from the cytosol by passive diffusion through the membrane after production inglycolysis.[183] Pyruvate is also made in the plastid from phosphoenolpyruvate, a metabolite made in the cytosol from pyruvate orPGA.[181] Acetate in the cytosol is unavailable for lipid biosynthesis in the plastid.[184] The typical length of fatty acids produced in the plastid are 16 or 18 carbons, with 0-3cis double bonds.[185]
The biosynthesis of fatty acids from acetyl-CoA primarily requires two enzymes. Acetyl-CoA carboxylase creates malonyl-CoA, used in both the first step and the extension steps of synthesis. Fatty acid synthase (FAS) is a large complex of enzymes and cofactors including acyl carrier protein (ACP) which holds the acyl chain as it is synthesized. The initiation of synthesis begins with the condensation of malonyl-ACP with acetyl-CoA to produce ketobutyryl-ACP. 2 reductions involving the use ofNADPH and one dehydration creates butyryl-ACP. Extension of the fatty acid comes from repeated cycles of malonyl-ACP condensation, reduction, and dehydration.[181]
A cross section of a leaf, showing chloroplasts in itsmesophyll cells. Stomal guard cells also have chloroplasts, though much fewer than mesophyll cells.
Distribution in a plant
Not all cells in a multicellular plant contain chloroplasts. All green parts of a plant contain chloroplasts as the color comes from thechlorophyll.[11] Theplant cells which contain chloroplasts are usuallyparenchyma cells, though chloroplasts can also be found incollenchyma tissue.[186] A plant cell which contains chloroplasts is known as achlorenchyma cell. A typicalchlorenchyma cell of a land plant contains about 10 to 100 chloroplasts.
In some plants such ascacti, chloroplasts are found in thestems,[187] though in most plants, chloroplasts are concentrated in theleaves. One squaremillimeter of leaf tissue can contain half a million chloroplasts.[11] Within a leaf, chloroplasts are mainly found in themesophyll layers of aleaf, and theguard cells ofstomata.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 lesschlorophyll. Chloroplasts can also be found in thebundle sheath cells of a leaf, especially inC4 plants, which carry out theCalvin cycle in their bundle sheath cells. They are often absent from theepidermis of a leaf.[162]
Cellular location
When chloroplasts are exposed to direct sunlight, they stack along theanticlinal cell walls to minimize exposure. In the dark they spread out in sheets along thepericlinal walls to maximize light absorption.
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'scell wall or turning sideways so that light strikes them edge-on. This reduces exposure and protects them fromphotooxidative damage.[188] 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.[189]Chloroplast movement is considered one of the most closely regulated stimulus-response systems that can be found in plants.[190]Mitochondria have also been observed to follow chloroplasts as they move.[191]
In higher plants, chloroplast movement is run byphototropins, blue lightphotoreceptors also responsible for plantphototropism. In some algae,mosses,ferns, andflowering plants, chloroplast movement is influenced by red light in addition to blue light,[188] 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.[191]
Studies ofVallisneria gigantea, an aquaticflowering 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 alongmicrofilament 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.[190][191]
Plastid types(Interactive diagram) Plants contain many different kinds of plastids in their cells.
Chloroplasts are a special type of a plant cell organelle called aplastid, 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 thezygote,[177] or fertilized egg. Proplastids are commonly found in an adult plant'sapical meristems. Chloroplasts do not normally develop from proplastids inroot tip meristems[192]—instead, the formation of starch-storingamyloplasts is more common.[177]
Inshoots, proplastids fromshoot apical meristems can gradually develop into chloroplasts inphotosynthetic leaf tissues as the leaf matures, if exposed to the required light.[15] This process involves invaginations of the inner plastid membrane, forming sheets of membrane that project into the internalstroma. These membrane sheets then fold to formthylakoids andgrana.[193]
Ifangiosperm shoots are not exposed to the required light for chloroplast formation, proplastids may develop into anetioplast stage before becoming chloroplasts. An etioplast is a plastid that lackschlorophyll, and has inner membrane invaginations that form a lattice of tubes in their stroma, called aprolamellar body. While etioplasts lack chlorophyll, they have a yellow chlorophyllprecursor stocked.[15] 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.[193]Gymnosperms do not require light to form chloroplasts.[193]
Light, however, does not guarantee that a proplastid will develop into a chloroplast. Whether a proplastid develops into a chloroplast some other kind of plastid is mostly controlled by thenucleus[15] and is largely influenced by the kind of cell it resides in.[177]
Many plastid interconversions are possible.
Plastid interconversion
Plastid differentiation is not permanent, in fact many interconversions are possible. Chloroplasts may be converted tochromoplasts, which arepigment-filled plastids responsible for the bright colors seen inflowers and ripefruit. Starch storingamyloplasts can also be converted to chromoplasts, and it is possible for proplastids to develop straight into chromoplasts. Chromoplasts and amyloplasts can also become chloroplasts, like what happens when acarrot or apotato is illuminated. If a plant is injured, or something else causes a plant cell to revert to ameristematic state, chloroplasts and other plastids can turn back into proplastids. Chloroplast, amyloplast, chromoplast, proplastid are not absolute; state—intermediate forms are common.[177]
Division
This sectionneeds expansion with: functions, Z-ring dynamic assembly, regulators such as Giant Chloroplast 1. You can help bymaking an edit requestadding to it.(February 2013)
Most chloroplasts in a photosynthetic cell do not develop directly from proplastids or etioplasts. In fact, a typicalshoot meristematic plant cell contains only 7–20proplastids. These proplastids differentiate into chloroplasts, which divide to create the 30–70 chloroplasts found in a mature photosynthetic plant cell. If the celldivides, chloroplast division provides the additional chloroplasts to partition between the two daughter cells.[194]
In single-celledalgae, 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 eachdaughter cell receives a mature chloroplast.[193]
Almost all chloroplasts in a cell divide, rather than a small group of rapidly dividing chloroplasts.[195] Chloroplasts have no definiteS-phase—their DNA replication is not synchronized or limited to that of their host cells.[196]Much of what we know about chloroplast division comes from studying organisms likeArabidopsis and the red algaCyanidioschyzon merolæ.[189]
Most chloroplasts in plant cells, and all chloroplasts inalgae arise from chloroplast division.[193]Picture references,[189][197]
The division process starts when the proteinsFtsZ1 andFtsZ2 assemble into filaments, and with the help of a proteinARC6, form a structure called a Z-ring within the chloroplast's stroma.[189][197] TheMin system manages the placement of the Z-ring, ensuring that the chloroplast is cleaved more or less evenly. The proteinMinD prevents FtsZ from linking up and forming filaments. Another proteinARC3 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.[189]
Next, the twoplastid-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.[189] The outer plastid-dividing ring is found wrapped around the outer chloroplast membrane. It consists of filaments about 5 nanometers across,[189] arranged in rows 6.4 nanometers apart, and shrinks to squeeze the chloroplast. This is when chloroplast constriction begins.[197] In a few species likeCyanidioschyzon merolæ, chloroplasts have a third plastid-dividing ring located in the chloroplast's intermembrane space.[189][197]
Late into the constriction phase,dynamin proteins assemble around the outer plastid-dividing ring,[197] helping provide force to squeeze the chloroplast.[189] Meanwhile, the Z-ring and the inner plastid-dividing ring break down.[197] During this stage, the many chloroplast DNA plasmids floating around in the stroma are partitioned and distributed to the two forming daughter chloroplasts.[198]
Later, the dynamins migrate under the outer plastid dividing ring, into direct contact with the chloroplast's outer membrane,[197] to cleave the chloroplast in two daughter chloroplasts.[189]
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.[197]
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.[197]
In this light micrograph of somemoss chloroplasts, some dumbbell-shaped chloroplasts can be seen dividing. Grana are also just barely visible as small granules.
In this light micrograph of somemoss chloroplasts, some dumbbell-shaped chloroplasts can be seen dividing. Grana are also just barely visible as small granules.
Chloroplast division In thislight micrograph of somemoss chloroplasts, many dumbbell-shaped chloroplasts can be seen dividing. Grana are also just barely visible as small granules.
Regulation
In species ofalgae that contain a single chloroplast, regulation of chloroplast division is extremely important to ensure that each daughter cell receives a chloroplast—chloroplasts can't be made from scratch.[91][189] In organisms like plants, whose cells contain multiple chloroplasts, coordination is looser and less important. It is likely that chloroplast and cell division are somewhat synchronized, though the mechanisms for it are mostly unknown.[189]
Light has been shown to be a requirement for chloroplast division. Chloroplasts can grow and progress through some of the constriction stages underpoor 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.[195][198]
Chloroplast inheritance
Likemitochondria, 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.[199]
Many mechanisms prevent biparental chloroplast DNA inheritance, including selective destruction of chloroplasts or their genes within thegamete orzygote, 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.[200]
Gymnosperms, such aspine trees, mostly pass on chloroplasts paternally,[201] whileflowering plants often inherit chloroplasts maternally.[202][203] Flowering plants were once thought to only inherit chloroplasts maternally. However, there are now many documented cases ofangiosperms inheriting chloroplasts paternally.[199]
Angiosperms, which pass on chloroplasts maternally, have many ways to prevent paternal inheritance. Most of them producesperm cells that 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.[199]
Among angiosperms, paternal chloroplast inheritance is observed more often inhybrids than in offspring from parents of the same species. This suggests that incompatible hybrid genes might interfere with the mechanisms that prevent paternal inheritance.[199]
Transplastomic plants
Recently, chloroplasts have caught attention by developers ofgenetically modified crops. Since, in most flowering plants, chloroplasts are not inherited from the male parent,transgenes in these plastids cannot be disseminated bypollen. This makesplastid transformation a valuable tool for the creation and cultivation of genetically modified plants that are biologically contained, thus posing significantly lower environmental risks. Thisbiological containment strategy is therefore suitable for establishing thecoexistence 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.[203]
Footnotes
^abNot to be confused withchromatophore—the pigmented cells in some animals—orchromatophore—the membrane associated vesicle in some bacteria.
^For this reason, glaucophyte chloroplasts are also known as 'muroplasts' from the Latinmuro meaning wall.
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