definition of endosymbiotic hypothesis

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Endosymbiotic Theory

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Endosymbiotic Theory Definition

Endosymbiotic theory is the unified and widely accepted theory of how organelles arose in organisms, differing prokaryotic organisms from eukaryotic organisms. In endosymbiotic theory, consistent with general evolutionary theory, all organisms arose from a single common ancestor. This ancestor probably resembled a bacteria, or prokaryote with a single strand of DNA surrounded by a plasma membrane. Throughout time, these bacteria diverged in form and function. Some bacteria acquired the ability to process energy from the environment in novel ways. Photosynthetic bacteria developed the pathways that enabled the production of sugar from sunlight. Other organisms developed novel ways to use this sugar is oxidative phosphorylation , which produced ATP from the breakdown of sugar with oxygen. ATP can then be used to supply energy to other reactions in the cell.

Both of these novel pathways led to organisms that could reproduce at a higher rate than standard bacteria. Other species, not being able to photosynthesis sugars or break them down through oxidative phosphorylation, decreased in abundance until they developed a novel adaptation of their own. The ability of endocytosis , or to capture other cells through the enfolding of the plasma membrane, is thought to have evolved around this time. These cells now had the ability to phagocytize , or eat, other cells. In some cells, the bacteria that were ingested were not eaten, but utilized. By providing the bacteria with the right conditions, the cells could benefit from their excessive production of sugar and ATP. One cell living inside of another is called endosymbiosis if both organisms benefit, hence the name of the theory. Endosymbiotic theory continues further, stating that genes can be transferred between the host and the symbiont throughout time.

This gives rise to the final part of endosymbiotic theory, which explains the variable DNA and double membranes found in various organelles in eukaryotes. While the majority of cell products start in the nucleus, the mitochondria and chloroplast make many of their own genetic products. The nucleus, chloroplasts, and mitochondria of cells all contain DNA of different types and are also surrounded by double membranes, while other organelles are surrounded by only one membrane. Endosymbiotic theory postulates that these membranes are the residual membranes from the ancestral bacterial endosymbiont. If a bacteria was engulfed via endocytosis, it would be surrounded by two membranes. The theory states that these membranes survived evolutionary time because each organism retained the maintenance of its membrane, even while losing other genes entirely or transferring them to the nucleus. Endosymbiotic theory is supported by a large body of evidence. The general process can be seen in the following graphic.

Endosymbiotic Theory Evidence

The most convincing evidence supporting endosymbiotic theory has been obtained relatively recently, with the invention of DNA sequencing. DNA sequencing allows us to directly compare two molecules of DNA, and look at their exact sequences of amino acids. Logically, if two organism share a sequence of DNA exactly, it is more likely that the sequence was inherited through common descent than the sequence arose independently. If two unrelated organisms need to complete the same function, the enzyme they evolve does not have to look the same or be from the same DNA to fill the same role. Thus, it is much more likely that organisms who share sequences of DNA inherited them from an ancestor who found them useful.

This can be seen when analyzing the mitochondrial DNA (mtDNA) and chloroplast DNA of different organisms. When compared to known bacteria, the mtDNA from a wide variety of organisms contains a number of sequences also found in Rickettsiaceae bacteria. Fitting with endosymbiotic theory, these bacteria are obligate intracellular parasites. This means they must live within a vesicle of an organism that engulfs them through endocytosis. Like bacterial DNA, mtDNA and the DNA in chloroplasts is circular. Eukaryotic DNA is typically linear. The only genes missing from the mtDNA and those of the bacteria are for nucleotide, lipid, and amino acid biosynthesis. An endosymbiotic organism would lose these functions over time, because they are provided for by the host cell.

Further analysis of the proteins, RNA and DNA left in organelles reveals that some of it is too hydrophobic to cross the external membrane of the organelle, meaning the gene could never get transferred to the nucleus, as the cell would have no way of importing certain hydrophobic proteins into the organelle. In fact, chloroplasts and mitochondria have their own genetic code, and their own ribosomes to produce proteins. These proteins are not exported from the mitochondria or chloroplasts, but are needed for their functions. The ribosomes of mitochondria and chloroplasts also resemble the smaller ribosomes of bacteria, and not the large eukaryotic ribosomes. This is more evidence that the DNA originated inside of the organelles, and is separate completely from the eukaryotic DNA. This is consistent with endosymbiotic theory.

Lastly, the position and structure of these organelles lends to the endosymbiotic theory. The mitochondria, chloroplasts, and nuclei of cells are all surrounded in double membranes. All three contain their DNA in the center of the cytoplasm, much like bacterial cells. Although less evidence exists linking the nucleus to any kind of extant species, both chloroplasts and mitochondria greatly resemble several species of intracellular bacteria, existing in much the same manner. The nucleus is thought to have arisen through enfolding of the cell membrane, as seen in the graphic above. Throughout the world, there are various endosymbiont bacteria, all of which live inside other organisms. Bacteria exist almost everywhere, from the soil to inside our gut. Many have found unique niches within the cells of other organisms, and this is the basis of endosymbiotic theory.

Related Biology Terms

• Endosymbiont – An organism that lives with another organism, cause both organisms to receive benefits.
• Cyanobacteria – Still extant, cyanobacteria are photosynthetic bacteria whose ancestors probably became the chloroplasts of plant cells.
• Proteobacteria – The bacterial ancestor to the mitochondria organelle.
• Eukaryote – An organism with membrane bound organelles, thought to have evolved from endosymbiotic interactions.

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Endosymbiotic theory

Endosymbiotic theory n., [ˌɛndəʊˌsɪmbɪˈəʊt.ɪk ˈθɪɚ.i] Definition: a theory proposing that the origin of organelles in eukaryotic cells is based on early endosymbiosis

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A eukaryotic cell is distinct from a prokaryotic cell by the presence of membrane-bound cellular structures called organelles. And based on this theory, the organelles mitochondria and chloroplasts are supposedly the early prokaryotic endosymbionts that had been taken in. They stayed inside the host cell for so long that they transitioned into those semi-autonomous organelles we know today.

Endosymbiotic Theory Definition

Endosymbiotic theory is one of the theories that are still prevalent to this day. It is a presumption that an endosymbiosis occurred between the early life forms. This form of symbiosis involves a larger cell that serves as a host and a smaller cell that is referred to as an endosymbiont .

In endosymbiotic theory, it posited that the larger cell engulfed or took in the smaller cell. The larger cell represents the eukaryotic cell of today whereas the smaller cell is the prokaryotic cell .

Watch this vid about endosymbiotic theory:

Endosymbiosis

Endosymbiosis is one of the many forms of symbiotic relationships (symbioses) that occur between or among organisms. In endosymbiosis, the endosymbiont lives within the body of its host. Endosymbiosis naturally occurs to this day. An example is a biological interaction between Rhizobium and the plant legumes.

Rhizobium is the endosymbiont that occurs within the roots of legumes and fixes atmospheric nitrogen into a form that is ready for use by the legume. The legume, in turn, provides Rhizobium metabolites such as malate and succinate from photosynthesis .

Endosymbiosis is the precept of the Endosymbiotic Theory, which was first conceptualized by botanist Konstantin Mereschkowski (4 August 1855 – 9 January 1921), and then backed up by scientific evidence by Lynn Margulis 1938–2011.

According to the Endosymbiotic Theory, endosymbiosis became the means by which organelles such as mitochondria and chloroplasts within eukaryotic cells came about. 1 Proponent of this theory posited that about 1.5 billion years ago a larger cell took in smaller free-living prokaryotes (bacteria) and inside the cell the prokaryote s lived as endosymbionts .

Research findings that seem to back up this theory implicate that the mitochondria arose from proteobacteria (such as SAR11 clade) 2 whereas the chloroplasts arose from cyanobacteria (particularly the nitrogen-fixing cyanobacteria). 3

The indication that this theory is plausible is based upon the same features shared by these organelles and their prokaryotic ancestors. Some of the characteristics common to them are as follows:

• Both mitochondria and plastids are capable of reproducing their own through a process akin to prokaryotic binary fission .
• Both mitochondria and plastids have single circular DNA similar to that of bacteria in terms of size and structure but different from that of the nucleus of the cell .
• Porins in the outer membranes of mitochondria and chloroplasts are similar to those in the bacterial cell membrane . Cardiolipin , a membrane lipid, is found only in the bacterial cell membrane and inner mitochondrial membrane.

Other Thoughts

Miller-urey experiment.

The age of the Earth is estimated to be around 4.54 billion years and life eventually existed and began about 3.5 billion years ago or earlier. The modern theory of abiogenesis holds that life on Earth began when the earliest living entities took in non-living materials.

They used these organic compounds to produce biomolecules and other building blocks of life. Biochemical processes, e.g. self-replication, self-assembly, autocatalysis, and cell membrane formation, probably led to the emergence of living entities. These processes were believed to be gradual and comprised of multiple events.

In the Miller-Urey experiment (i.e., Stanley Miller and Harold Urey), the results indicated that the simulated-primitive Earth favored the chemical syntheses of the fundamental structures of the cell membrane. Mixing gases methane, ammonia, hydrogen, and water and then electrically-sparking them resulted in the formation of amino acids .

Prebiotic soup

Around four billion years ago, the Earth was hostile to life. No life forms could exist due to the harsh conditions. Eventually, simple organic compounds formed.

The hypothetical model of the early Earth with conditions that led to the synthesis of simple organic compounds is called the prebiotic (primordial) soup . Alexander Oparin 1894–1980 and John Burdon Sanderson Haldane 1892–1964 were the ones to conceive this idea and independently formulated theories that collectively became the heterotrophic origin of life theory .

Both of them theorized that the early Earth’s atmosphere was a chemically reducing atmosphere. It aided in producing such organic compounds . As these compounds were produced, they accumulated and formed a so-called prebiotic soup . Through time, these simple organic compounds transformed into more complex organic polymers.

In the long run, life came about. The first life entities took in and used organic molecules to thrive and survive in the prebiotic soup. They theorized that the first forms of life were heterotrophic . Recent evidence, though, suggests that autotrophs are likely the first organisms .

RNA World hypothesis

The four major biomolecules essential to life are nucleic acids (e.g. RNA , DNA ), carbohydrates (various sugars), lipids (fats), and amino acids (constituents of proteins). Primitive life is hypothesized to be RNA-based since RNA could be both genetic material and a catalyst. The transitioning of primitive life forms into single-celled living things occurred gradually for many million years.

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Further reading.

Prokaryotic Ancestor of Mitochondria: on the hunt

• The Evolution of Cell Organelles
• endosymbiosis. (n.d.). Collins English Dictionary – Complete & Unabridged 10th Edition. Retrieved from Dictionary.com website http://dictionary.reference.com/browse/endosymbiosis.
• “Mitochondria Share an Ancestor With SAR11, a Globally Significant Marine Microbe”. (2011). Retrieved from ScienceDaily Link.
• Deusch, O.; et al. (2008). “Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor”. Mol. Biol. Evol 25 : 748–761

© Biology Online. Content provided and moderated by Biology Online Editors

Last updated on June 30th, 2023

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The Endosymbiotic Theory

The endosymbiotic theory is a scientific theory that proposes that some of the organelles in the eukaryotic cells, such as mitochondria and chloroplast , have originated from free-living prokaryotes ( bacteria and archaea ). Endosymbiosis is the relationship between two organisms when one lives within the other organism, eventually benefiting both partners.

The endosymbiotic theory explains that when one organism, typically a microbe, takes up residence within the cell of another organism, over time, they form a close relationship that can be advantageous for both partners. The larger host cell provides a protected environment and essential nutrients. At the same time, the internalized microbe contributes its specialized functions, often becoming an organelle within the host cell.

The theory was conceptualized first by Konstantin Mereschkowsk in 1905 and then supported with evidence by Lynn Margulis in 1967.

The Theory of Endosymbiosis in Timeline

The German botanist Heinrich Anton de Bary coined the term ‘Symbiose’ to designate this coexistence. The concept of symbiosis , that two different organisms stably coexist and even give rise to a new type of organism, is attributed to Simon Schwendener.

19th Century

• In 1905, Russian biologist Konstantin Mereschkowski suggested that the origin of eukaryotic cells involved the engulfment of smaller prokaryotic cells.
• Around the same time, German botanist Andreas Schimper proposed that chloroplasts in plant cells might have originated from independent photosynthetic organisms.

1960s-1970s

• In 1967, Lynn Margulis proposed that eukaryotic cells, with their complex structures and organelles, resulted from symbiotic relationships between ancestral prokaryotic cells. He argued that mitochondria, the cellular powerhouses, were once free-living bacteria capable of aerobic respiration . Similarly, she suggested that chloroplasts originated from photosynthetic bacteria that became incorporated into host cells. 

1980s-1990s

• Researchers discovered striking similarities between the DNA of organelles like mitochondria and chloroplasts and the DNA of modern-day bacteria.
• Protists like single-celled organisms are found to host certain bacteria fixing nitrogen (nitrogen-fixing bacteria).

2000s-Present

•  In the 21st Century, endosymbiosis forms the basis of the origin of mitochondria, chloroplast, and other organelles. It also explains the development of complex multicellular organisms and the coevolution of symbiotic partners.

The Process of Endosymbiosis

According to the endosymbiotic theory, the symbiotic origin of eukaryotic cells is a multi-event process.

1. Primary Endosymbiosis

It refers to the initial engulfment of a free-living bacterium by a host cell, creating a new organelle within the host cell. The most prominent examples of primary endosymbiosis are the origin of mitochondria and chloroplasts; both were once free-living cells. Here, two membranes surround the organelles; the inner is obtained from the bacterium, and the outer is derived from the host cell.

• Origin of Mitochondria : A eukaryotic cell engulfed a bacterium capable of aerobic respiration. This bacterium provides a valuable energy source through respiration. Over time, the host cell and the engulfed bacterium developed a mutually beneficial relationship. The bacterium became the mitochondrion, retaining its own DNA and membrane structure while working in tandem with the host cell.
• Origin of Chloroplasts : Here, an ancestral host cell captured a photosynthetic bacterium, which could convert sunlight into energy through photosynthesis . As with mitochondria, a symbiotic partnership formed, with the photosynthetic bacterium evolving into the chloroplast. It allowed the host cell to harness the power of photosynthesis for energy production.

2. Secondary Endosymbiosis

It involves a eukaryotic cell engulfing another eukaryotic cell already undergoing primary endosymbiosis. This secondary engulfment results in a more complex cellular arrangement, leading to the diversification of eukaryotic lineages and the emergence of new types of organelles.

• Formation of Plastids : These organelles involved in photosynthesis are found in various algae and plants. Different groups of algae have acquired plastids through secondary endosymbiosis, which consists of the engulfment of photosynthetic eukaryotic cells. In contrast to the two membranes of primary organelles, four membranes surround chloroplasts obtained by secondary endosymbiosis. In most cases, the nucleus of the engulfed cell disappears, with the remains of this nucleus still found lying between the two pairs of membranes. This structure is called a nucleomorph.

Thus, the endosymbiotic theory explains the presence of double-membraned organelles within protists.

Evidence that Supports the Endosymbiotic Theory

There are several proofs to support the Endosymbiotic Theory. However, the discovery of independent DNA (from the host) in mitochondria and chloroplasts supported the theory the most. The other evidences are as follows:

• Structural Similarities : Mitochondria and chloroplasts share structural characteristics with free-living bacteria, such as double membranes and DNA. Both the organelles are almost of the same size as the bacterial cell.
• Reproduction : Mitochondria and chloroplasts replicate within the cell independently, similar to how bacteria reproduce.
• Genetic Evidence : The DNA within mitochondria and chloroplasts is more similar to bacterial DNA than the host cell’s nucleus.
• Evolutionary Relationships : Analysis of genetic sequences shows that mitochondria and chloroplasts are more closely related to specific groups of bacteria than eukaryotic cells.

However, the statement that mitochondria and chloroplasts are much larger than prokaryotic cells does not support the endosymbiotic theory.

What is the Importance of the Endosymbiotic Theory

It is important because the theory explains the origin of the eukaryotic cells. It also describes how chloroplast and mitochondria might have originated from once free-living prokaryotes. This understanding has reshaped our perception of how fundamental cellular organelles came to be and how multicellular life forms arose.

The endosymbiotic theory also highlights how cooperation and symbiosis have played pivotal roles in shaping cellular evolution.

• Endosymbiosis – Ib.bioninja.com.au
• Endosymbiosis and the Evolution of Eukaryotes – Bio.libretexts.org
• Endosymbiotic Theories forEukaryote Origin – Royalsocietypublishing.org
• Endosymbiosis – Evolution.berkeley.edu
• Endosymbiosis: The Feeling is Not Mutual – Ncbi.nlm.nih.gov
• Endosymbiosis – Cell.com

Article was last reviewed on Tuesday, October 3, 2023

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Cooperation: working together toward the same goal.

Lipid: a building block of life (molecule) made from smaller pieces (fatty acids). There are several kinds of lipids - fats, waxes, sterols,...  more

Slime molds are a great example of cooperation among cells. Click for more detail.

It’s good to be friendly with your neighbors, right? Individuals and communities do better if they help each other out. Cooperation isn’t just important for humans; without a bit of interaction with neighbors, life as we know it would not exist.

The earliest living neighbors on our planet were all single-celled creatures. Some of the neighboring single-cells joined and began living together as one organism, one inside the other. This partnership was so successful that it led to the evolution of many of the life forms on our planet, including humans.

What is a Cell?

All living things are made up of cells . Even though there are many millions of life forms on earth, all of them are made up of only two basic types of cell: prokaryotes and eukaryotes.

Cells contain DNA . Prokaryotes (pro-carry-oats) are small and simple and have rings of circular DNA floating free inside the cell. Eukaryotes (you-carry-oats) are large and more complex. They have a nucleus, which holds strings of linear DNA within a lipid membrane. All the life forms that you are used to seeing – animals (including humans), plants, and fungi – are made up of eukaryotic cells. The bacteria, which are too small to see without a microscope, are made up of prokaryotic cells.

A prokaryotic cell. Click for more detail.

Prokaryotic cells were some of the earliest life forms on earth. They first appear in the fossil record around 4 billion years ago. Prokaryotes were around for a long, long time before eukaryotic cells appeared around 1.8 billion years ago. This has led us to think that the ancestor of all eukaryotic cells was a prokaryote.

But to get from a prokaryote to a eukaryote, the cell needed to become a lot more complicated. Eukaryotic cells are powered by special organelles, which work a bit like batteries. All eukaryotes have an organelle called the mitochondrion, which makes energy to power the cell. Plant cells have another type of organelle called a plastid. Plastids can harvest energy from sunlight, like a solar battery. Chloroplasts are a type of plastid. 

What is Endosymbiotic Theory?

How did the eukaryotes become so complicated? And where did these battery-like organelles come from?

We think we know part of the answer. Eukaryotic cells may have evolved when multiple cells joined together into one. They began to live in what we call symbiotic relationships. The theory that explains how this could have happened is called endosymbiotic theory. An endosymbiont is one organism that lives inside of another one. All eukaryotic cells, like your own, are creatures that are made up of the parts of other creatures.

Mitochondria, the important energy generators of our cells, evolved from free-living cells. Click for more detail.

The mitochondrion and the chloroplast are both organelles that were once free-living cells. They were prokaryotes that ended up inside of other cells (host cells). They may have joined the other cell by being eaten (a process called phagocytosis), or perhaps they were parasites of that host cell.

Rather than being digested by or killing the host cell, the inner cell survived and together they thrived. It’s kind of like a landlord and a tenant. The host cell provides a comfortable, safe place to live and the organelle pays rent by making energy that the host cell can use. This happened a long time ago, and over time the organelle and the host cell have evolved together. Now one could not exist without the other. Today they function as a single organism, but we can still find evidence of the free-living past of the organelles if we look closely.

What Evidence Supports Endosymbiotic Theory?

As early as 1883, botanist Andreas Schimper was looking at the plastid organelles of plant cells using a microscope. He watched the plastids divide and noticed something odd. The process looked very similar to the way some free-living bacteria divided.

During the 1950s and 60s, scientists found that both mitochondria and plastids inside plant cells had their own DNA. It was different from the rest of the plant cell DNA. When scientists looked closer at the genes in the mitochondrial and plastid DNA, they found that the genes were more like those from prokaryotes. This tells us that organelles are more closely related to prokaryotes.

The green chloroplasts in this cell are now a critical part of plant cells, but they evolved from an entirely different organism than the plant cell. The chloroplast is thought to have evolved from a cyanobacterial cell that managed to survive the cell's defenses.

We know that multiple membranes surround the organelles too. If we look at the molecules of those membranes, they look like the membranes that surround modern day free-living prokaryotes.

So, organelles have their own DNA, and their genes are very similar to the genes of modern-day prokaryotes. They have membranes that look like those of prokaryotes, and they also seem to divide and replicate in similar ways. If a eukaryotic cell loses an organelle, it cannot remake it. Each eukaryote cell has to inherit at least one copy of an organelle from its parent cell if it is to live. That means that the genetic information needed to make the organelles is not found in the DNA of the eukaryotic cell. All of this evidence supports the theory that the organelles came from outside the eukaryotic cell. We think it tells us that they were once free-living prokaryotes.

Eukaryotic cells have many structures not found in prokaryotic cells.

A scientist named Lynn Margulis put all of this information together and published it in 1967. Her paper is called “On the origin of mitosing cells”. Mitosing cells are eukaryotes. Today scientists know her paper is very important, but it took many years before they accepted her theory.

But our story of the evolution of eukaryotic cells is far from complete. We haven’t talked at all about the other structures that we can find in eukaryotic cells but not in prokaryotic cells, and how they evolved. These include the nucleus, Golgi apparatus, endoplasmic reticulum, lysosomes, and cytoskeleton.

Where did they come from? The truth is we are still not sure. They could have evolved over time within the eukaryotic cells. Or, they could also be the result of other ancient endosymbiotic events. How they evolved is a problem that still needs to be solved. 

Additional images via Wikimedia Commons. Filamentous cyanobacteria via Sally Warring.

Read more about: Cells Living in Cells

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• Publisher: Arizona State University School of Life Sciences Ask A Biologist
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• Date published: February 24, 2016
• Date accessed: August 28, 2024
• Link: https://askabiologist.asu.edu/explore/cells-living-in-cells

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Endosymbiotic Theory: How Eukaryotic Cells Evolve

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The endosymbiotic theory is the accepted mechanism for how eukaryotic cells evolved from prokaryotic cells . It involves a cooperative relationship between two cells which allow both to survive—and eventually led to the development of all life on Earth.

Endosymbiotic Theory History

First proposed by Boston University biologist Lynn Margulis in the late 1960s, the Endosymbiont Theory proposed that the main organelles of the eukaryotic cell were actually primitive prokaryotic cells that had been engulfed by a different, bigger prokaryotic cell .

Margulis' theory was slow to gain acceptance, initially facing ridicule inside mainstream biology. Margulis and other scientists continued work on the subject, however, and now her theory is the accepted norm within biological circles.

During Margulis' research on the origin of eukaryotic cells, she studied data on prokaryotes, eukaryotes, and organelles, finally proposing that similarities between prokaryotes and organelles, combined with their appearance in the fossil record, was best explained by something called "endosymbiosis" (meaning "to cooperate inside.")

Whether the larger cell provided protection for the smaller cells, or the smaller cells provided energy to the larger cell, this arrangement seemed to be mutually beneficial to all of the prokaryotes.

While this sounded like a far-fetched idea at first, the data to back it up is undeniable. The organelles that seemed to have been their own cells include the mitochondria and, in photosynthetic cells, the chloroplast. Both of these organelles have their own DNA and their own ribosomes that do not match the rest of the cell. This indicates that they could survive and reproduce on their own.

In fact, the DNA in the chloroplast is very similar to photosynthetic bacteria called cyanobacteria. The DNA in the mitochondria is most like that of the bacteria that causes typhus.

Before these prokaryotes were able to undergo endosymbiosis, they first most likely had to become colonial organisms. Colonial organisms are groups of prokaryotic, single-celled organisms that live in close proximity to other single-celled prokaryotes.

Advantage to Colony

Even though the individual single-celled organisms remained separate and could survive independently, there was some sort of advantage to living close to other prokaryotes. Whether this was a function of protection or a way to get more energy, colonialism has to be beneficial in some manner for all of the prokaryotes involved in the colony.

Once these single-celled living things were within close enough proximity to one another, they took their symbiotic relationship one step further. The larger unicellular organism engulfed other, smaller, single-celled organisms. At that point, they were no longer independent colonial organisms but instead were one large cell.

When the larger cell that had engulfed the smaller cells started to divide, copies of the smaller prokaryotes inside were made and passed down to the daughter cells.

Eventually, the smaller prokaryotes that had been engulfed adapted and evolved into some of the organelles we know of today in eukaryotic cells such as the mitochondria and chloroplasts.

Other Organelles

Other organelles eventually arose from these first organelles, including the nucleus where the DNA in a eukaryote is housed, the endoplasmic reticulum and the Golgi apparatus.

In the modern eukaryotic cell, these parts are known as membrane-bound organelles. They still do not appear in prokaryotic cells like bacteria and archaea but are present in all organisms classified under the Eukarya domain.

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Endosymbiotic hypothesis

The endosymbiotic hypothesis suggests that certain organelles, particularly mitochondria and chloroplasts, originated as free-living bacteria that were engulfed by ancestral eukaryotic cells. This theory explains the presence of double membranes and their own DNA in these organelles.

5 Must Know Facts For Your Next Test

• Mitochondria and chloroplasts have their own circular DNA similar to bacterial genomes.
• These organelles reproduce independently within the cell through a process resembling binary fission.
• The double membrane structure of mitochondria and chloroplasts supports the idea of an engulfing event.
• Ribosomes found in mitochondria and chloroplasts are more similar to bacterial ribosomes than to eukaryotic ones.
• Endosymbiosis is believed to be a key event in the evolution of complex eukaryotic cells from simpler prokaryotic ancestors.

Review Questions

• What evidence supports the endosymbiotic hypothesis for the origin of mitochondria?
• How does the reproduction method of mitochondria and chloroplasts support the endosymbiotic hypothesis?
• Why is the similarity between mitochondrial/chloroplast ribosomes and bacterial ribosomes significant?

Related terms

Eukaryote : A type of cell with a nucleus enclosed within membranes, distinct from prokaryotes.

Prokaryote : A unicellular organism that lacks a nucleus and membrane-bound organelles.

Binary Fission : A form of asexual reproduction in which a cell divides into two genetically identical cells.

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Microbe Notes

Endosymbiosis- Definition, 5 Examples, Theory, Significances

Endosymbiosis is the association in which one cell resides inside the other cell, and they have a mutual interaction of benefitting and getting benefitted.

Symbiosis is the relationship between organisms where both of them depend on each other without harming and utilizing the sources they have to survive. The word endo indicates that this relationship occurs inside the organism where one of them lives within the body of the other.

Symbiosis is of two types based on the location of the organism:

• Endosymbiosis
• Ectosymbiosis

The organisms that show endosymbiosis are called endosymbionts. The other cell or organisms in which they reside are called hosts. 

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Interesting Science Videos

Some Examples of Endosymbionts

The endosymbiotic relationship exists in many species of organisms, such as plants, bacteria, protists, algae, insects, and vertebrates. Some of them are mentioned below:

• Rhizobium is a nitrogen-fixing bacteria that reside in the root nodules of leguminous plants. It gets benefits by extracting nutrients from the cell and benefits the plants by providing them with nitrogenous compounds. 
• Acyrthosiphon pisum, an aphid type of insect , and its endosymbiont are bacteria, i.e., Buchnera spp.
• Symbiodinium (a dinoflagellate) resides in mollusks and corals. They help in the coral reef formation as they aid in receiving and storing the sunlight along with some nutrients providing the required energy for the deposition of the carbonates.
• Diatoms (such as Hemialus ) in the oceans and seas require nitrogen which is fixed by the endosymbiotic bacterium (such as Richelia ) residing in it.
• Algae of Oophila spp have an endosymbiotic relationship with the salamander of Ambystoma spp.

Endosymbiotic Theory

It is the explanation of how eukaryotic cells evolved from prokaryotic cells. It also explains how the eukaryotic cells acquired some organelles, which were prokaryotes, specifically the mitochondrion and chloroplasts . This theory was first presented by a botanist named Konstantin Mereschkowski in the year 1905 to 1910.

Endosymbiotic Theory Steps

• To begin with, the cell initially had the presence of rudimentary endoplasmic reticulum and a rudimentary nuclear envelope formed by the infolding of the plasma membrane.
• Then one of these early cells engulfed aerobic bacteria. Aerobic bacteria can utilize oxygen and provide the cell with energy in the form of ATP . The process involved in engulfing those bacteria is called endophagocytosis, in which the plasma membrane folds inside to form vesicles and transport the bacteria inside the cell.
• After generations and generations (maybe millions) of the engulfment of the bacteria, its descendants gradually lost their ability to live independently, and they became the internal symbionts of the large host cell. This led to the formation of an organelle that we call mitochondrion.
• Again one of the host cells engulfed another bacterial cell which was a photosynthetic cyanobacterium. After many generations of bacteria, it gradually became dependent on the host cell, and another cell organelle formed, which we call the chloroplast.

As there were two symbiotic events, one followed by the other, therefore this phenomenon is also called serial endosymbiosis.

How the Scientists found the order of the formation of mitochondrion and chloroplast?

In the endosymbiotic theory, it is stated that the mitochondrion formation occurred initially, and later on the chloroplast. This order was determined by using the knowledge of phylogeny or evolutionary history. 

As the bacteria are prokaryotes, they do not have the presence of mitochondria, and chloroplast. Almost all the eukaryotes after that such as protozoa, animals, fungi, plants, and algae have mitochondria suggesting that aerobic bacterium was engulfed very early so mitochondrion was considered to evolve at first in the eukaryotic cells. 

Chloroplasts are present in only a few types of eukaryotic cells, mainly algae, and plants. This suggests that the cyanobacterium was engulfed by a most recent ancestor of the plants and algae after the ancestor split off in other directions from the lineages which led to protozoa, animals, and fungi. This suggests that the chloroplast was formed later.

Evidence that Shows the Existence of Endosymbiosis in Eukaryotic Cells

The evolution of cells to eukaryotic is believed due to the involvement of endosymbiosis of organelles such as plastids, and mitochondria (that were initially prokaryotes) which later on formed the complex eukaryotic cells.

•  The cell organelles such as chloroplast, and mitochondria can divide binary fission which might have been separate at first and later symbiotically entered the eukaryotic cell.
• The size of bacterial and those cell organelles is similar.
• The presence of an extra outer membrane may be due to the vesicular transport of these cells into the eukaryotic cell.
• Along with the 80s ribosomes, there is also the presence of the 70s ribosomes which are common in prokaryotes.
• As in the prokaryotes, mitochondria, and chloroplast also have circular and naked DNA.
• The cell organelles also show susceptibility toward some antibiotics such as Chloramphenicol which is the characteristic of bacterial cells.

Endosymbiosis Significances

• The endosymbiont gets a favorable environment for its survival.
• The hosts consume different nutrients which are required by the endosymbiont for their growth, multiplication, and survival.
• The hosts also get some benefits such as some nutrients and anti-pathogenic chemicals from the endosymbiont. For eg. In the case of E. coli , it releases chemicals called colicin which can harm other pathogens entering the human body.
• Endosymbiosis process is also beneficial in the evolution of cells, where one cell moved inside the other and gradually developed into a complex cellular structure. Different forms of life or organisms that currently exist are because of endosymbiosis.

Some Related Terms

Ectosymbiosis: It is the phenomenon in which one organism on the surface or skin or outer body part of another organism and they both have a mutually beneficial relationship. The organisms that show ectosymbiosis are called ectosymbionts.

Protocoopeartion: It is similar to symbiosis but not obligatory.

Commensalism: It is a type of relationship in which one of the members is benefitted while the other is neither benefitted nor harmed. The organisms that show commensalism are called commensals.

Parasitism: It is a type of relationship in which one organism is benefitted while another is harmed due to the presence of that member called a parasite.

• Nowack, Eva C M, and Michael Melkonian. “Endosymbiotic associations within protists.”  Philosophical Transactions of the Royal Society of London. Series B, Biological sciences  vol. 365,1541 (2010): 699-712.
• Moran N.A., and Chong R.A.  (2018) Endosymbiosis. Evolutionary Biology. Doi: 10.1093/OBO/9780199941728-0114
• Martin W.F., Garg S., and Zimorski V. (2015) Endosymbiotic Theories of Eukaryote Origin. Phil. Trans. R. Soc. B 370: 20140330
• Lynn M. (2011), Symbiogenesis. A New Principle of Evolution Rediscovery. Palaentological Journal. 44 (12): 1525-1539.

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Syllabus Edition

First teaching 2014

Last exams 2024

Endosymbiotic Theory ( DP IB Biology: SL )

Revision note.

Endosymbiotic Theory

Endosymbiosis.

• Endosymbiosis is where one organism lives within another
• If the relationship is beneficial to both organisms the engulfed organism is not digested
• For endosymbiosis to occur one organism must have engulfed the other by the process of endocytosis

Endosymbiotic theory

• The endosymbiotic theory is used to explain the origin of eukaryotic cells . The evidence provided for this theory comes from the structure of the mitochondria and chloroplasts
• Scientists have suggested that ancestral prokaryote cells evolved into ancestral heterotrophic and autotrophic cells through the following steps:
• To overcome a small SA:V ratio ancestral prokaryote cells developed folds in their membrane. From these infoldings organelles such as the nucleus and rough endoplasmic reticulum formed
• This gave the larger prokaryote a competitive advantage as it had a ready supply of ATP and gradually the cell evolved into the heterotrophic eukaryotes with mitochondria that are present today
• At some stage in their evolution, the heterotrophic eukaryotic cell engulfed a smaller photosynthetic prokaryote. This cell provided a competitive advantage as it supplied the heterotropic cell with an alternative source of energy , carbohydrates
• Over time the photosynthetic prokaryote evolved into chloroplasts and the heterotrophic cells into autotrophic eukaryotic cells

The endosymbiotic theory - an explanation for the evolution of eukaryotic cells

Evidence to support the endosymbiotic theory

• Both reproduce by binary fission
• Both contain their own circular, non-membrane bound DNA
• They both transcribe mRNA from their DNA
• They both have 70S ribosomes to synthesise their own proteins
• They both have double membranes

Learn how the structure of the mitochondria and chloroplast support the endosymbiotic theory.

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Understanding Evolution

Your one-stop source for information on evolution

Endosymbiosis

Evidence for endosymbiosis.

Biologist Lynn Margulis first made the case for endosymbiosis in the 1960s, but for many years other biologists were skeptical. Although Jeon watched his amoebae become infected with the x-bacteria and then evolve to depend upon them, no one was around over a billion years ago to observe the events of endosymbiosis. Why should we think that a mitochondrion used to be a free-living organism in its own right? It turns out that many lines of evidence support this idea. Most important are the many striking similarities between prokaryotes (like bacteria) and mitochondria:

• Membranes  — Mitochondria have their own cell membranes, just like a prokaryotic cell does.

When you look at it this way, mitochondria really resemble tiny bacteria making their livings inside eukaryotic cells! Based on decades of accumulated evidence, the scientific community supports Margulis’s ideas: endosymbiosis is the best explanation for the evolution of the eukaryotic cell.

What’s more, the evidence for endosymbiosis applies not only to mitochondria, but to other cellular organelles as well.  Chloroplasts  are like tiny green factories within plant cells that help convert energy from sunlight into sugars, and they have many similarities to mitochondria. The evidence suggests that these chloroplast organelles were also once free-living bacteria.

The endosymbiotic event that generated mitochondria must have happened early in the history of eukaryotes, because all eukaryotes have them. Then, later, a similar event brought chloroplasts into some eukaryotic cells, creating the lineage that led to plants.

Despite their many similarities, mitochondria (and chloroplasts) aren’t free-living bacteria anymore. The first eukaryotic cell evolved more than a billion years ago. Since then, these organelles have become completely dependent on their host cells. For example, many of the key proteins needed by the mitochondrion are imported from the rest of the cell. Sometime during their long-standing relationship, the genes that code for these proteins were transferred from the mitochondrion to its host’s genome. Scientists consider this mixing of genomes to be the irreversible step at which the two independent organisms become a single individual.

Paramecium bursaria , a single-celled eukaryote that swims around in pond water, may not have its own chloroplasts, but it does manage to “borrow” them in a rather unusual way.  P. bursaria  swallows photosynthetic green algae, but it stores them instead of digesting them. In fact, the normally clear paramecium can pack so many algae into its body that it even looks green! When  P. bursaria  swims into the light, the algae photosynthesize sugar, and both cells share lunch on the go. But  P. bursaria doesn’t exploit its algae. Not only does the agile paramecium chauffeur its algae into well-lit areas, it also shares the food it finds with its algae if they are forced to live in the dark.

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Endosymbiosis: the feeling is not mutual

Patrick j. keeling.

1 Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, ON, Canada M5G 1Z8

2 Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada, Tel. +1 604 822 4906, Fax. +1 604 822 6089

John P. McCutcheon

3 Division of Biological Sciences, University of Montana, Missoula, Montana 59812

Endosymbiosis was an idea that provided a remarkable amount of explanatory power to observations about eukaryotic organelles. But it also promoted a few assumptions that have been less well-examined, and here we look at two of these. The first is the idea that some endosymbiotic relationships that are assumed to be mutualistic, such as nutritional symbioses and eukaryotic organelles, are not in fact power struggles mush as we assume many other ecological interactions to be. The second is that endosymbiotic merger between organelles and their hosts involved the acquisition of a great many genes that took on functions in the host. New data from other endosymbiotic systems and the organelles themlseves suggest some of our hypotheses about organelle origins and distribution may be misled by the expectation that such genes exist and persist in large numbers.

Introduction: Untangling what we know and what we assume about endosymbiosis

The idea is old and appealingly simple: dissimilar organisms live together and by doing so become more than they were as individuals ( De Bary, 1879 ; Sagan, 1967 ). They become a symbiosis. It is clear that symbioses have propelled associations of organisms into environments where the individuals alone could not survive, and by doing so have massively affected the evolution of life ( Archibald, 2014 ). But what is less clear is how entering into symbiosis affects the participating organisms. Symbioses are often described as mutualisms, or relationships where both partners benefit. (In fact, the word symbiosis itself is sometimes used interchangeably with mutualism.) But the benefits for both partners are sometimes hard to see. Indeed, mutualisms have been previously likened to symbioses that have simply found a way to manage the inherent conflicts of interests between organisms ( Herre et al., 1999 ). This is especially true in endosymbioses, which can often look remarkably one-sided ( Bennett and Moran, 2015 ; Garcia and Gerardo, 2014 ; Kiers and West, 2016 ).

In this paper we use symbiosis in its most general sense. That is, we define it simply as any sustained organismal interaction somewhere on the pathogenic-beneficial continuum ( Lewis, 1985 ). We highlight several recent examples that expose how the evolutionary interests of endosymbionts can become misaligned, and how endosymbioses that seem extremely interdependent and stable (even “permanent”) can break down under the right circumstances. In particular, we focus on two aspects of endosymbiosis that affect our thinking of evolution more broadly: the idea that endosymbiosis is often a mutualistic relationship, and the idea that endosymbiosis has a deep and lasting an impact on the genome evolution through endosymbiotic gene transfer.

Endosymbiosis as an antagonistic relationship: Context matters

Putting aside the classic organelles, the mitochondria and plastids, the vast majority of endosymbioses are probably pathogenic. That is, the presence of a microbe inside a host cell most often imposes a cost from the host perspective. If this is true, it follows that most endosymbioses that are beneficial from the host perspective likely evolved from interactions that were initially pathogenic, or at least mildly so. This idea is supported by analyses of the origins of proteobacterial symbionts with various hosts, which shows that the vast majority of beneficial proteobacterial symbionts have evolved from pathogenic ancestors ( Sachs et al., 2014 ). What is required for an endosymbiosis to shift from costly to beneficial from the host perspective? Quite simply, the ecological context must change so that the benefits of the interaction outweigh the costs. The ecological context shifts that seem most common in endosymbiosis are those involving hosts gaining access to previously inaccessible nutrition or energy, or those where hosts defend themselves in ways not possible without the presence of the symbiont.

In endosymbioses where the microorganism provides energy or nutrition for the host, such as the mitochondrion, plastid, and many nutritional symbionts in insects, the context shift is absolute and (nearly, seemingly) permanent: the host cannot survive in the environment without its symbiont. These sorts of massive ecological context shifts drive the most spectacular and long-term types of symbiosis, because the host must preserve the symbiont at all costs (or get a new endosymbiont, acquire the function in some other way, or move to a new environment). The long-term and strictly dependent nature of these symbioses can make the context dependency hard to see, because loss of endosymbiont without a change in host context results in extinction of the entire symbiosis. However, the context dependency of symbiosis is often clear in symbioses that are relatively recent associations, such as protists and their photosynthetic symbionts ( Lowe et al., 2016 ) or amoebae and their bacterial symbionts ( DiSalvo et al., 2015 ). But recent work provides a few instances where long-term endosymbioses—the type perhaps more naturally thought of as mutualisms—seem to be in the process of breaking down or have actually proceeded to eliminate their endosymbiont.

We can gain some insight into the way we instinctively think about endosymbiosis by considering the case of an insect endosymbiont called Hodgkinia cicadicola . Hodgkinia is in many ways a typical insect nutritional endosymbiont. It provides cicadas with two of the ten amino acids that they cannot make on their own and that are not provided at high levels in the strict plant sap diet of the insect (the remaining 8 essential amino acids are provided by another bacterial endosymbiont called Sulcia ; McCutcheon et al., 2009 ). In many cicada species, this clean narrative is preserved: Hodgkinia provides two essential amino acids, Sulica provides the other eight, and the host gives them a nice place to live. Everyone is happy, and from some perspectives it looks like a three-way mutualism.

But this tidy story starts to break down in other cicada species. In some cicadas, the single ancestral Hodgkinia lineage has fragmented into two new distinct cell types, each with a distinct genome that has lost genes so that both are required by the host to provide the nutrition required by the ancestral single lineage ( Van Leuven et al., 2014 ). Put another way, a host that used to have to keep track of two bacterial lineages ( Sulcia and a single Hodgkinia lineage) now is required to keep track of three. Why does this happen? It isn’t clear yet, but we suspect that it is related to the unusual, long, and variable life cycles of cicadas. Documented cicada life cycles are between 2 and 17 years, and we know that in a short-lived species there is one Hodgkinia lineage, and that in the longest-lived cicada species there are several dozen Hodgkinia lineages ( Campbell et al., 2015 ). These long-lived cicadas must therefore cope with numerous Hodgkinia lineages, each one encoding just a few genes.

While vertical transmission normally promotes cooperation between host and symbiont ( Bull et al., 1991 ; Ewald, 1987 ), this cooperation seems to be breaking down in some cicada groups despite an unchanged vertical transmission route. What has changed? We suspect that the high mutation rate of Hodgkinia combined with the increased symbiont generations that become possible in long-lived cicadas increases the genetic diversity of the symbiont population and thus promotes competition (or selfishness) and limits cooperation. Less fit symbiont genotypes can rise to high frequency during long cicada generations and occasionally get fixed, in an event we see as a split lineage ( Van Leuven et al., 2014 ). From the host perspective, this process is probably nonadaptive. It is not better to transmit dozens of Hodgkinia lineages to each egg instead of one, but the host has little recourse (outside of symbiont replacement) because its ecological context requires the two amino acids that Hodgkinia still produces. The cicada is stuck in a symbiont rabbit hole of its own making ( Bennett and Moran, 2015 ).

What makes Hodgkinia different from a classical intracellular parasite such as the malaria parasite, Plasmodium ? We argue it is primarily context—or, different only in the direction in which the hostility is aimed. For Plasmodium , the simple narrative is the infectious agent is forcing itself into a cell, disrupting its normal function and subverting it to its own purpose. Ultimately the infectious agent kills and discards its host to move on to take over the next hapless victim. In the case of Hodgkinia , the story initially seems more like a nurturing embrace of one cell by another, the bacterium enveloped by its host, allowing it to shed functions that are no longer needed because essential nutrients and energy are all readily donated by its new benefactor. But when the context changes—in this case, the host life cycle—the cooperation between host and symbiont breaks down. The selfish tendencies of Hodgkinia were always there, they were just held in check by the host.

We suggest that endosymbiotic interactions are best thought of not as mutualistic “happily ever-after” stories, but instead as “use it up and cast it off” situations that are stable for variable lengths of time. Endosymbiosis nearly always produces dead ends for one of the two partners—in the case of Plasmodium and other traditional parasites, the host is the partner that is cast off in the short term, but in the case of Hodgkinia and other beneficial endosymbionts it is the symbiont that is cast off in the longer term. In one case the symbiont is exploiting the host, while in the other the host is exploiting the symbiont. But neither one is mutualistic: they are both power relationships that differ simply based on whether the internal or external partner is in control.

This logic suggests that endosymbiotic relationships will always be temporary and they will be lost or replaced, but don’t we already know this is not true? The answer depends on the time scale one considers, and the amount of diversity one has studied. For example, a taxonomically narrow view of the bacteria-in-bacteria mealybug symbiosis might lead one to conclude that this baroque structure has only evolved once, but a view with a wider taxonomic breadth and depth reveals frequent endosymbiont turnover ( Husnik and McCutcheon, 2016 ). But what about eukaryotic organelles? Are they not the classic case of endosymbiosis leading to “happily ever after”? It’s clear that the host has control, so why has the endosymbiont not burned itself out like Hodgkinia seems to be doing? Why have organelles not been replaced with fresh symbionts? It could be that organelle degeneration has stabilized due to large amounts of gene transfer and protein-targeting. But it is also clear that if the core function of the organelles is acquired independently or side-stepped somehow, that even this “permanent” relationship can be lost. Indeed, photosynthesis has been lost scores of times in plastids and oxidative phosphorylation and electron transport has been lost many times in mitochondria when the host’s ecological context has changed such that these functions were no longer required ( Burki, 2016 ; Müller et al., 2012 ; van der Giezen, 2009 ; Williams and Keeling, 2003 ). As highly valuable as these functions are, they are not core functions of these organelles. Instead, the core function of mitochondria, the last function to be retained in even the most reduced organelle, is iron-sulfur cluster assembly ( Müller et al., 2012 ; van der Giezen, 2009 ; Williams and Keeling, 2003 ). In the case of plastids, the core function is likely different in different lineages, but fatty acid, amino acid, heme, and isoprenoid biosynthesis are all candidates in different groups which have lost photosynthesis ( Foth and McFadden, 2003 ; Williams and Keeling 2003 ; Keeling, 2013 ; Ralph et al., 2001 ). But recent studies that have considered eukaryotic diversity more broadly show that even these core functions have sometimes been lost, and when they are, the association breaks down and the endosymbiont is eliminated ( Gornik et al., 2015 ; Janouškovec et al., 2015 ; Karnkowska et al., 2016 ). Moreover, in the dinoflagellates, where photosynthesis and even plastids are particularly prone to loss, we see occasional cases of plastid replacement: apparently when one plastid is used up and discarded, another one can be acquired to replace it ( Keeling, 2013 ; Archibald, 2015 ). These studies show that even organelles have not been frozen into permanence, it just seems that way because we have not looked broadly enough (or waited long enough). The degenerative ratchet is still slowly turning, even in organelles.

Overall, when we mentally distinguish “cooperation” and “competition”, it is a mistake to apply the kind of thinking that we intuitively glean from the relationship within macroorganism symbioses such as cleaner wrasses and fish to the rather more abstract relationship we observe between one cell living within another (although they may be more similar after all, since context-dependent breakdown of the wrasse-fish mutualism is observed: Gingins et al., 2013 ). Instead, we argue that endosymbioses are rarely, if ever, mutualistic. Endosymbioses are just different forms of competition, where the vector of control points in different directions with different magnitudes depending on the context. One partner is always in control, or fighting to increase control. Coexistence can occur for long periods of time, but if conditions change the partnership can quickly tip towards extinction for either the subordinate member or the entire symbiosis. The interesting questions for long term endosymbiosis, like eukaryotic organelles, therefore shift from why and how the partnership formed, to why and how the partnership has so far avoided extinction.

Genomic impacts of endosymbiosis

The endosymbiotic origin of mitochondria and plastids primed us to accept similar explanations for other phenomena. At the cellular level, this initially led to a rush to explain other organelles in endosymbiotic terms, for example the flagella and cilia, peroxisomes, endoplasmic reticulum, and even the nucleus ( Cavalier-Smith, 1987 ; Gupta, 1999 ; Lake and Rivera, 1994 ; Margulis, 1970 ; Sagan, 1967 ). Endosymbiotic explanations for these organelles has gone out of fashion due to an ongoing absence of evidence ( Keeling, 2014 ; Martin, 1999 ), but the fashion has made a comeback to explain genomic data. The acceptance that mitochondria and plastids were indeed derived from endosymbiotic bacteria came at an auspicious time in the early days of molecular biology and subsequently genomics. These technologies were revolutionary, broke down a lot of long held ideas, and lead to an intellectual vacuum to be filled with new explanations. At least some of this vacuum was naturally filled by explanations involving endosymbiosis ( Keeling, 2014 ); some of these explanations have now formed the foundations for other assumptions, but have not been subjected to serious critical examination.

Most important of these is a prevalent idea that by looking at the evolutionary history of genes in a genome we can “see” an ancient endosymbiosis based on the presence of genes in the host that were acquired from that endosymbiont. This presupposes that an endosymbiont will donate genes to the nucleus of its host, an idea with a complex history. Almost simultaneously with Margulis’ influential paper in The Journal of Theoretical Biology ( Sagan, 1967 ), Goksøyr outlined a similar hypothesis in Nature ( Goksøyr, 1967 ), and went further suggesting that the endosymbiont would have moved some of its genes to the host, and that their products would then be targeted back to the endosymbiont. Weeden (1981) developed this idea further, going as far as to say it was a necessary corollary to the endosymbiont hypothesis because organelle genomes were insufficient to encode the necessary genes to support organelle function. Although the exact origin of all nucleus-encoded organelle genes has been questioned ( Keeling, 2013 ; Larkum et al., 2007 ), these two ideas have provided enormous explaining power when looking at organelle biology and evolution. However, beyond this well-tested core is a less-well-examined idea that is nevertheless influential. The thinking goes that if a large number of genes were transferred to the host for proteins now targeted back to the organelle, then probably a lot of other genes were transferred as well. Many of these proteins, if not most, are now not targeted back to the organelle but acquired functions in the host.

This seems reasonable enough - genes were flowing, and if they are potentially useful then it stands to reason the host should keep some to function in cytosolic pathways, and maybe even keep a lot. Early studies supported this conclusion based on genomic data from model systems (e.g., Martin et al., 1998 ). Naturally, the implications of this conclusion can be extrapolated to touch on other, more complex problems. Most importantly, if organelle endosymbionts donated a lot of genes for now-cytosolic proteins, then we should be able to “see” evidence for now-lost organelles in the nuclear genomes of their erstwhile hosts. This idea rests on the assumption that, because these genes have acquired a function independent of the organelle, they will be retained even when the organelle is lost or replaced.

If true, this would be a powerful tool in the reconstruction of evolutionary history, and has formed the logical basis for a number of claims for ancient endosymbiotic events and cryptic or now-lost organelles. For example, in work on plastid organelles, such studies have concluded that non-photosynthetic lineages like oomycetes or ciliates once had a red algal plastid ( Reyes-Prieto et al., 2008 ; Tyler et al., 2006 ), or that red algal plastid-containing lineages once had green algal plastids ( Moustafa et al., 2009 ; Woehle et al., 2011 ). These conclusions have been challenged on the basis of the veracity of the phylogenetic results ( Burki et al., 2012 ; Deschamps and Moreira, 2012 ; Moreira and Deschamps, 2014 ), but the idea itself has not been challenged particularly, and has had a major impact on models for the evolution of organelles and on how we perceive the impact of endosymbiosis on the host genome and cellular function. Indeed, it emphasizes the importance of endosymbiosis on both counts: it predicts more endosymbiotic organelles in evolution and ascribes more functional impact to them. However, these conclusions are dependent on an assumption (that organelle derived genes will be kept in large numbers when the organelle is lost) that is itself built on another assumption (that those genes were transferred and retained in the first place), and neither has been thoroughly tested. In the almost two decades since the original analyses supporting the presence of large-scale transfers of genes from the organelle endosymbiont for proteins that do not function in the organelle (e.g., Martin et al., 1998 ), there have been significant advances that would allow this important conclusion to be reexamined with more confidence. We are now awash with recent genomic data from a variety of eukaryotes, and phylogenetic methods and computational power both now allow for significantly better tests of a gene’s origin. Some studies support an overall episodic influx of genes that is consistent with this idea (e.g., Ku et al., 2015 ), but other studies on relatively recent secondary and tertiary endosymbiotic events find the number of endosymbiont-derived genes in the host nucleus that that are not functionally linked to the organelle to be few, or even potentially zero ( Burki et al., 2012 ; Curtis et al., 2012 ; Hehenberger et al., 2016 ; Moreira and Deschamps, 2014 ; Patron et al., 2006 ). Different endosymbiotic events may have had different impacts, but if the assumption is untrue, or even if significant variation is found in different organelle origins, then it will limit the extent that we can interpret the presence or absence of such genes from a nuclear genome. This in turn impacts how much weight can be given to endosymbiosis to explain eukaryotic diversity.

Acknowledgments

We thank Ford Doolittle for discussions over a long period of time, and the Canadian Institute for Advanced Research (CIFAR) and the US National Academies of Science for supporting a Sackler Colloquium in 2014 that led to many useful interactions. PJK and JPM are Senior Fellows of CIFAR.

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