Chloroplast

• 1. Introduction

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  A chloroplast is a type of organelle that quietly performs one of the most consequential chemical transformations on Earth: converting sunlight into the sugar that fuels nearly all plant life. But what is it, exactly, and where did it come from? The answer turns out to be stranger than most people expect. Chloroplasts were not invented by plants. They were captured. Roughly two billion years ago, a free-living cyanobacterium was engulfed by an early eukaryotic cell. Instead of being digested, it persisted inside its host, and over time became the photosynthetic engine we now find in every leaf, every blade of grass, every sprig of algae. That ancient partnership is still running today. And the story of how scientists came to understand it, from a grain of green pigment spotted in 1837 to the sequencing of chloroplast DNA in 1986, raises questions that reach into every branch of life on the planet. How did one ancient engulfment event give rise to such bewildering diversity? And why do some organisms still carry chloroplasts that have completely lost the ability to photosynthesize?

• 2. A Captured Cyanobacterium

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  Around two billion years ago, a free-living cyanobacterium entered an early eukaryotic cell. Whether it arrived as food or as an internal parasite, it managed to escape the vacuole meant to contain it and survive inside the host. The cyanobacterium offered something valuable in return: sugar from photosynthesis. Over an immense span of time, the arrangement tightened. Many of the cyanobacterium's genes were either lost or transferred into the nucleus of the host cell. The host, now in control, began shipping proteins back into what had once been an independent organism. The closest living relative of that original engulfed cyanobacterium is thought to be Gloeomargarita lithophora. With one striking exception, every chloroplast on Earth traces back to that single event. That exception is Paulinella chromatophora, a photosynthetic amoeboid that independently acquired an endosymbiotic cyanobacterium from the genus Synechococcus somewhere between 90 and 140 million years ago. Paulinella's chromatophore has a genome of about one million base pairs, which is roughly one third the size of Synechococcus genomes and encodes around 850 proteins. By contrast, most chloroplast genomes are typically around 150,000 base pairs. Because Paulinella's acquisition happened so much more recently, scientists study it to understand what the earliest stages of chloroplast evolution looked like.

• 3. Layers on Layers

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  Chloroplasts obtained through a single engulfment have two surrounding membranes, both inherited from the original cyanobacterium's gram-negative cell wall. But many organisms acquired chloroplasts by a second route: engulfing an alga that already contained a primary chloroplast. This secondary endosymbiosis added membranes to the structure. A secondary chloroplast can end up with three or four membranes, depending on how much of the original alga was retained. In organisms like Cryptomonas and the chlorarachniophytes, a remnant of the swallowed alga's nucleus persists between the second and third membranes as a nucleomorph. Some organisms pushed the process even further. Dinoflagellates in the genera Karlodinium and Karenia lost their original red algal chloroplast and replaced it with one taken from a haptophyte, making those plastids tertiary acquisitions. The diatom-engulfing dinoflagellates Kryptoperidinium and Durinskia carry a diatom endosymbiont so minimally reduced that it retains its own mitochondria, endoplasmic reticulum, ribosomes, and nucleus. Diatoms have been engulfed by dinoflagellates at least three times. In some of these genera, the original three-membraned peridinin chloroplast still exists alongside the newcomer, converted into an eyespot.

• 4. A Genome in Miniature

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  Chloroplast DNA was identified biochemically in 1959 and confirmed by electron microscopy in 1962. It was first sequenced in 1986. Most chloroplast genomes are single circular DNA molecules, typically 120,000 to 170,000 base pairs long and weighing roughly 80 to 130 million daltons. The ancestral cyanobacterium that gave rise to chloroplasts probably had a genome of over 3,000 genes. Contemporary chloroplast genomes retain only around 100. In land plants, roughly 11 to 14 percent of the DNA in cell nuclei can be traced back to the chloroplast, reaching as high as 18 percent in Arabidopsis, corresponding to about 4,500 protein-coding genes. Of the approximately 3,000 proteins found in chloroplasts, around 95 percent are now encoded by nuclear genes. Many chloroplast genomes contain two inverted repeats, which are highly conserved in land plants and accumulate few mutations. Similar inverted repeats appear in cyanobacteria and in the glaucophyte and rhodophyte chloroplast lineages, suggesting the structure predates the chloroplast itself. The physical DNA inside living cells does not always match the tidy circular map drawn by geneticists; the molecules take on a range of linear, branching, and other complex forms that researchers do not yet fully understand.

• 5. The Four Lineages

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  All primary chloroplasts belong to one of four lineages. Three of them, the glaucophytes, the rhodophytes (red algae), and the chloroplastida (green algae and land plants), share a single ancestral endosymbiotic event and are grouped together as Archaeplastida. The fourth is Paulinella. The glaucophyte lineage is the smallest, with only 25 described species. These chloroplasts diverged earliest, and they carry features that connect them to their cyanobacterial ancestors. Glaucophyte chloroplasts still have a peptidoglycan cell wall, a type of wall otherwise found only in bacteria, which is why they are called muroplasts. Their thylakoids remain unstacked and surround a carboxysome, an icosahedral structure housing the carbon-fixing enzyme RuBisCO. Red algal chloroplasts, or rhodoplasts, carry a pigment called phycoerythrin, which gives many red algae their characteristic color, though the combination of phycoerythrin with the blue-green chlorophyll a produces hues ranging from reddish to purple. In deep water, phycoerythrin helps absorb the limited light available; red algae living in shallow water have less of it and can appear greenish. Green chloroplasts, in contrast, have lost their phycobilisomes and gained chlorophyll b, which together with chlorophyll a produces the color associated with most plant life. Green chloroplasts also store starch inside the organelle rather than outside it.

• 6. Structure from the Inside Out

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  In land plants, chloroplasts are generally lens-shaped, measuring 3 to 10 micrometers in diameter and 1 to 3 micrometers thick. Corn seedling chloroplasts are approximately 20 cubic micrometers in volume. Algae show far greater variety in chloroplast shape, from net-like structures in Oedogonium to cup-shaped forms in Chlamydomonas to ribbon-like spirals in Spirogyra. Inside every chloroplast, beyond the outer and inner membranes, lies a semi-gel-like fluid called the stroma. Floating within it is the thylakoid system, a highly dynamic collection of interconnected membranous sacks. In most vascular plants, thylakoids are stacked into structures called grana, each of which can contain anywhere from two to roughly one hundred thylakoids, though stacks of 10 to 20 are most common. The three-dimensional architecture of this system was debated for years; a 2019 study determined that features from both the prevailing helical model and the competing bifurcation model are reconciled by left-handed helical membrane junctions discovered in that work. Embedded in the thylakoid membranes are photosystem I, photosystem II, and ATP synthase. ATP synthase works much like a turbine, harnessing the flow of hydrogen ions back out of the thylakoid space to generate ATP in the stroma. The protein-dense stroma also holds RuBisCO, which is probably the most abundant protein on the planet.

• 7. More Than Photosynthesis

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  Apicomplexan parasites such as Plasmodium, the malaria parasite, carry a vestigial red algal derived chloroplast called an apicoplast that has lost all photosynthetic function and retains no photosynthetic pigments or true thylakoids. Yet apicomplexans die when this organelle's function is disrupted. Apicoplasts synthesize fatty acids, isopentenyl pyrophosphate, iron-sulfur clusters, and carry out part of the heme pathway. The most critical of these is isopentenyl pyrophosphate synthesis; when apicomplexans are grown in a medium rich in isopentenyl pyrophosphate, they jettison the organelle entirely. This demonstrates that chloroplasts carry out important functions well beyond sugar production. In plants, chloroplasts participate directly in immune defense. When a pathogen is detected, chloroplasts deliberately damage their own photosynthetic machinery to produce reactive oxygen species. High concentrations of these molecules trigger the hypersensitive response, in which infected cells seal themselves off and die. Lower concentrations initiate systemic acquired resistance, sending chemical signals through the plant. Chloroplasts also synthesize all the fatty acids in a plant cell; linoleic acid, one of those fatty acids, is a precursor to the defense molecule jasmonate. In some plants, chloroplasts migrate toward infection sites and toward the nucleus when an attack is underway, acting as cellular sensors for the broader immune network.