Chloroplast

A chloroplast is a type of organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. Chloroplasts have a high concentration of chlorophyll pigments which capture the energy from sunlight and convert it to chemical energy and release oxygen. The chemical energy created is then used to make sugar and other organic molecules from carbon dioxide in a process called the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in some unicellular algae, up to 100 in plants like Arabidopsis and wheat.
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 photosynthetic cyanobacterium that was engulfed by an early eukaryotic cell.
Chloroplasts evolved from an ancient cyanobacterium that was engulfed by an early eukaryotic cell. Because of their endosymbiotic origins, chloroplasts, like mitochondria, contain their own DNA separate from the cell nucleus. With one exception, all chloroplasts can be traced back to a single endosymbiotic event. Despite this, chloroplasts can be found in extremely diverse organisms that are not directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events.

Discovery and etymology

The first definitive description of a chloroplast was given by Hugo von Mohl in 1837 as discrete bodies within the green plant cell. In 1883, Andreas Franz Wilhelm Schimper named these bodies as "chloroplastids". In 1884, Eduard Strasburger adopted the term "chloroplasts".
The word chloroplast is derived from the Greek words chloros, which means green, and plastes, which means "the one who forms".

Endosymbiotic origin of chloroplasts

Chloroplasts are one of many types of organelles in photosynthetic eukaryotic cells. They evolved from cyanobacteria through a process called organellogenesis. Cyanobacteria are a diverse phylum of gram-negative bacteria capable of carrying out oxygenic photosynthesis. Like chloroplasts, they have thylakoids. The thylakoid membranes contain photosynthetic pigments, including chlorophyll a. This origin of chloroplasts was first suggested by the Russian biologist Konstantin Mereschkowski in 1905 after Andreas Franz Wilhelm Schimper observed in 1883 that chloroplasts closely resemble cyanobacteria. Chloroplasts are only found in plants, algae, and some species of the amoeboid Paulinella.
Mitochondria are thought to have come from a similar endosymbiosis event, where an aerobic prokaryote was engulfed.

Primary endosymbiosis

Approximately twobillion years ago, a free-living cyanobacterium entered an early eukaryotic cell, either as food or as an internal parasite, but managed to escape the phagocytic vacuole it was contained in and persist inside the cell. This event is called endosymbiosis, or "cell living inside another cell with a mutual benefit for both". The external cell is commonly referred to as the host while the internal cell is called the endosymbiont. The engulfed cyanobacteria provided an advantage to the host by providing sugar from photosynthesis. Over time, the cyanobacterium was assimilated, and many of its genes were lost or transferred to the nucleus of the host. Some of the cyanobacterial proteins were then synthesized by host cell and imported back into the chloroplast, allowing the host to control the chloroplast.
Chloroplasts which can be traced back directly to a cyanobacterial ancestor are known as primary plastids. Chloroplasts that can be traced back to another photosynthetic eukaryotic endosymbiont are called secondary plastids or tertiary plastids.
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, chloroplasts arose from a single endosymbiotic event around twobillion years ago and these chloroplasts all share a single ancestor. It has been proposed that the closest living relative of the ancestral engulfed cyanobacterium is Gloeomargarita lithophora. Separately, somewhere about 90–140 million years ago, this process happened again in the amoeboid Paulinella with a cyanobacterium in the genus Prochlorococcus. This independently evolved chloroplast is often called a chromatophore instead of a chloroplast.
Chloroplasts are believed to have arisen after mitochondria, since all eukaryotes contain mitochondria, but not all have chloroplasts. This is called serial endosymbiosis—where an early eukaryote engulfed the mitochondrion ancestor, and then descendants of it then engulfed the chloroplast ancestor, creating a cell with both chloroplasts and mitochondria.

Secondary and tertiary endosymbiosis

Many other organisms obtained chloroplasts from the primary chloroplast lineages through secondary endosymbiosis—engulfing a red or green alga with a primary chloroplast. These chloroplasts are known as secondary plastids.
As a result of the secondary endosymbiotic event, secondary chloroplasts have additional membranes outside of the original two in primary chloroplasts. In secondary plastids, typically only the chloroplast, and sometimes its cell membrane and nucleus remain, forming a chloroplast with three or four membranes—the two cyanobacterial membranes, sometimes the eaten alga's cell membrane, and the phagosomal vacuole from the host's cell membrane.
The genes in the phagocytosed eukaryotes nucleus are often transferred to the secondary host's nucleus. Cryptomonas and chlorarachniophytes retain the phagocytosed eukaryotes nucleus, an object called a nucleomorph, located between the second and third membranes of the chloroplast.
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.
Still other organisms, including the dinoflagellates Karlodinium and Karenia, obtained chloroplasts by engulfing an organism with a secondary plastid. These are called tertiary plastids.
File:Chloroplast Cladogram.svg|alt=Cladogram of chloroplast evolution|center|thumb|800x800px|Possible cladogram of chloroplast evolution Circles represent endosymbiotic events. For clarity, dinophyte tertiary endosymbioses and many nonphotosynthetic lineages have been omitted.
----^a It is now established that Chromalveolata is paraphyletic to Rhizaria.

Primary chloroplast lineages

All primary chloroplasts belong to one of four chloroplast lineages—the glaucophyte chloroplast lineage, the rhodophyte chloroplast lineage, and the chloroplastida chloroplast lineage, the amoeboid Paulinella chromatophora lineage. The glaucophyte, rhodophyte, and chloroplastidian lineages are all descended from the same ancestral endosymbiotic event and are all within the group Archaeplastida.

Glaucophyte chloroplasts

The glaucophyte chloroplast group is the smallest of the three primary chloroplast lineages as there are only 25 described glaucophyte species. Glaucophytes diverged first before the red and green chloroplast lineages diverged. Because of this, they are sometimes considered intermediates between cyanobacteria and the red and green chloroplasts. This early divergence is supported by both phylogenetic studies and physical features present in glaucophyte chloroplasts and cyanobacteria, but not the red and green chloroplasts. First, glaucophyte chloroplasts have a peptidoglycan wall, a type of cell wall otherwise only in bacteria. Second, glaucophyte chloroplasts contain concentric unstacked thylakoids which surround a carboxysome – an icosahedral structure that contains the enzyme RuBisCO responsible for carbon fixation. Third, starch created by the chloroplast is collected outside the chloroplast. Additionally, like cyanobacteria, both glaucophyte and rhodophyte thylakoids are studded with light collecting structures called phycobilisomes.

Rhodophyta (red chloroplasts)

The rhodophyte, or red algae, group is a large and diverse lineage. Rhodophyte chloroplasts are also called rhodoplasts, literally "red chloroplasts". Rhodoplasts have a double membrane with an intermembrane space and phycobilin pigments organized into phycobilisomes on the thylakoid membranes, preventing their thylakoids from stacking. Some contain pyrenoids. Rhodoplasts have chlorophyll a and phycobilins for photosynthetic pigments; the phycobilin phycoerythrin is responsible for giving many red algae their distinctive red color. However, since they also contain the blue-green chlorophyll a and other pigments, many are reddish to purple from the combination. The red phycoerythrin pigment is an adaptation to help red algae catch more sunlight in deep water—as such, some red algae that live in shallow water have less phycoerythrin in their rhodoplasts, and can appear more greenish. Rhodoplasts synthesize a form of starch called floridean starch, which collects into granules outside the rhodoplast, in the cytoplasm of the red alga.

Chloroplastida (green chloroplasts)

The chloroplastida group is another large, highly diverse lineage that includes both green algae and land plants. This group is also called Viridiplantae, which includes two core clades—Chlorophyta and Streptophyta.
Most green chloroplasts are green in color, though some aren't due to accessory pigments that override the green from chlorophylls, such as in the resting cells of Haematococcus pluvialis. Green chloroplasts differ from glaucophyte and red algal chloroplasts in that they have lost their phycobilisomes, and contain chlorophyll b. They have also lost the peptidoglycan wall between their double membrane, leaving an intermembrane space. Some plants have kept some genes required for the synthesis of peptidoglycan, but have repurposed them for use in chloroplast division instead. Chloroplastida lineages also keep their starch inside their chloroplasts. In plants and some algae, the chloroplast thylakoids are arranged in grana stacks. Some green algal chloroplasts, as well as those of hornworts, contain a structure called a pyrenoid, that concentrate RuBisCO and CO in the chloroplast, functionally similar to the glaucophyte carboxysome.
There are some lineages of non-photosynthetic parasitic green algae that have lost their chloroplasts entirely, such as Prototheca, or have no chloroplast while retaining the separate chloroplast genome, as in Helicosporidium. Morphological and physiological similarities, as well as phylogenetics, confirm that these are lineages that ancestrally had chloroplasts but have since lost them.