Image shows an embryonic stem cell

Endosymbiosis: Evidence and Application in the Study of Disease

Darwin documented natural selection among finches while in the Galapagos Islands. With his new knowledge, Darwin proposed his theory of evolution. He claimed that evolution was essentially descent with modification. With time, scientists adapted the definition of evolution. Evolution is now regarded as natural selection, leading to descent with modification. There is no doubt that Darwin’s theory laid the groundwork for studying evolution. However, many are unaware of endosymbiosis. This theory concerns unicellular organisms that roamed the Earth long before the complex, multicellular finches. After all, endosymbiosis is paramount in understanding cell biology and descent with modification.

What is the theory of endosymbiosis?

“Endo” refers to something internal. “Symbiosis” is defined as an interaction between two organisms. There are various types of symbiotic relationships; mutualism, commensalism, and parasitism. Mutualism is a symbiotic relationship that benefits both species. Commensalism only benefits one species, while the other is unaffected. Also, parasitism only benefits one species. But, one species is harmed by the other in this relationship. Therefore, endosymbiosis is when a symbiotic organism lives within another organism. 

Endosymbiosis refers to species, but the theory of endosymbiosis does not refer to species. Instead, the theory concerns organelles. Lynn Margulis, hypothesized endosymbiosis regarding the mitochondria, chloroplast (in plant cells), and basal bodies (part of flagella). Her adaptation to this theory, first suggested by Ivan Wallen in the 1920s, stated that these organelles were once unicellular organisms, and they became engulfed by early eukaryotic cells. 

Portrait of Lynn Margulis
Lynn Margulis, an American biologist. Image Source:

In the subsequent sections, this blog post will briefly discuss the difference between prokaryotic and eukaryotic cells. Following this information, this blog will present evidence of endosymbiosis regarding mitochondria and chloroplasts. The summation of the information provided will discuss the implications of endosymbiosis for evolutionary theory. 

Prokaryotic vs. Eukaryotic Cells

Prokaryotic cells and eukaryotic cells share few similarities and differ from each other in numerous ways. Both cell types have similar features for structure, a cytoskeleton, and cytoplasm to fill up the intracellular space. Prokaryotes and eukaryotes also have ribosomes, the organelles responsible for synthesizing proteins. Aside from these few similarities, these cell types vary greatly in size, structure, and composition.

Prokaryotic Cells

Prokaryotic cells are small cells (< 5 micrometers in diameter) and are individual unicellular organisms, including bacteria and archaea. Because of their small size, these cells have DNA condensed into plasmids, small ribosomes, submicroscopic flagella, and the absence of much of the organelles found in eukaryotic cells. In addition, prokaryotic cells do not undergo mitosis for reproduction. Instead, they only reproduce asexually through binary fission. One feature of prokaryotic cells that is only common in some eukaryotic cells is cell walls. Autotrophic organisms have a cell wall, but the cell walls in prokaryotes are more complex. Their complexity lies in their composition. Prokaryote cell walls consist of peptidoglycan, as opposed to structural hydrocarbons in autotrophic organisms. 

A typical prokaryotic cell involved in endosymbiosis
A typical prokaryotic cell. These cells do not have many components. Image Source: Khan Academy

Eukaryotic Cells

Eukaryotic cells are much larger than prokaryotic cells, ranging from 10 to 100 micrometers in diameter. Therefore, they have more room for organelles. Eukaryotes have endoplasmic reticulums, Golgi, microtubules, lysosomes, mitochondria, and chloroplasts (in autotrophs), to name a few. Eukaryotic cells make up a multicellular organism, such as animals and plants, and reproduce via mitosis (asexual reproduction). Meiosis occurs through sexual reproduction and allows for genetic variation between different generations. Moreover, one can observe some of the features of prokaryotes in eukaryotes, except on a larger scale. For example, they have more DNA. Eukaryotic DNA wraps around histone proteins, allowing for correct gene expression. Gene expression varies because some of the DNA is a 10-nanometer fiber with more exposure, while the rest is a 30-nanometer fiber with less exposure. Eukaryotes also have larger ribosomes for more diverse gene expression and larger flagella, which propel the larger cell. 

A eukaryotic cell, involved in endosymbiosis
A typical eukaryotic cell. Eukaryotes have more organelles compared to prokaryotes. Image Source: Khan Academy

Evidence Supporting the Endosymbiotic Theory

According to Margulis’ theory, mitochondria and chloroplasts are all unicellular organisms. Hence, they were all smaller than early eukaryotic cells, were more simple, and contained less DNA. Based on these organelles, evidence for the endosymbiotic theory follows, and their role in evolution. 

The Mitochondria

The mitochondria generate adenosine triphosphate (ATP) for the cell. ATP holds great potential energy within its phosphodiester bonds, released when forming adenosine diphosphate (ADP). Proteins serve the purpose of assisting and catalyzing metabolic processes. The mitochondria alone can code for up to 63 proteins but harbor on the order of 2000 proteins (Zimorski, V. et al., 2014). There is a discrepancy in the number of proteins. How can an organelle only code for 63 proteins but have the potential of creating 2000? Researchers Zimorski et al. owe this discrepancy to endosymbiotic gene transfer. 

Mitochondria organelle found in a cell
A labeled diagram of a mitochondrion. Notably, the mitochondrion has segments of DNA. Image Source:

Endosymbiotic Gene Transfer

Repositioning of genes occurs during endosymbiotic transfer (Zimorski, V. et al., 2014). During this process, genes relocate from the mitochondria to the chromosomes of the host cell. Cytosolic proteins express many of the genes associated with the mitochondria. As a result, these cytosolic proteins double as signaling molecules for the mitochondria (Zimorski, V. et al., 2014). As the expression of mitochondrial genes occurs outside of the mitochondria, the nuclear genome expands (Zimorski, V. et al., 2014). 

Bioenergetics in Eukaryotic Evolution

Different mitochondrial genes are related to varying origins. For example, some genes have high concentrations of adenine and thymine. Therefore, scientists trace these genes to adenine and thymine-rich proteobacteria (Zimorski, V. et al., 2014). Other scientists have traced the lineage of eukaryotes to simpler archaea. Either way, the energy-producing cristae of mitochondria enable the complexities of eukaryotic cells. 

Though scientists are still gathering scientific facts concerning the origin of mitochondria, there are some widely debated hypotheses about the additional roles the mitochondria play in the cell. A research review conducted by Lynch and Marinov has collected data concerning the relationships between the mitochondria and cell characteristics. As the cell’s surface area increases in micrometers, the surface area of the mitochondrion also increases (Lynch, M., & Marinov, G. K., 2017). In addition, an increased surface area of a mitochondrion correlates to an increase in the number of ATP synthase complexes located on the organelle (Lynch, M., & Marinov, G. K. 2017). ATP synthase is the protein responsible for creating a proton gradient that fuels the phosphorylation of ATP to ADP.

A Mutualistic Relationship

Since there are more mitochondria and more ATP molecules in cells with a larger volume (eukaryotes), more ATP is available for metabolic processes. Therefore, eukaryotic cells become more complex with more bioenergetic membranes. Ribosomes have much to do with the complexity of the eukaryotic cells. They assemble the proteins needed for gene expression. But, with ATP molecules, the operation of individual genes is commonplace and evolutionary modifications of genes are more frequent (Lynch, M., & Marinov, G. K. 2017). Ribosomes and mitochondria are both indicators of a cell’s abilities. 

Mitochondria had a mutualistic relationship with the host cell before becoming reliant on the host cell. Martin and Müller (1998) have hypothesized the benefits reaped within the relationship. They believed that mitochondria provided the cell with hydrogen by-products needed in methanogenesis (Martin W, Müller M., 1998). In return, the host cell provided needed resources to the mitochondria (Martin W, Müller M., 1998). The mitochondria would otherwise have obtained these resources from the environment.  


Chloroplasts share some characteristics with mitochondria. Like mitochondria, they have circular DNA and experience binary fission. Additionally, chloroplast genes are integrated into the nuclear genome of early eukaryotic cells through endosymbiotic gene transfer. These factors align with prokaryote characteristics. But, chloroplasts have additional features that further support the endosymbiotic theory. 

This image shows a labeled chloroplast from a eukaryotic cell.
A labeled diagram of a chloroplast. Image source:

Phylogenic Analysis of Chloroplast Endosymbiosis 

To discover evidence of endosymbiosis in chloroplasts, scientists observed chloroplast-encoding genes. Associations between enzyme families and homolog genes allow for phylogenic analysis. Scientists examined enzymes involved in the production of fatty acids and lipids, part of chloroplast membranes. The results are as follows. 

Phylogenic Trees showing endosymbiosis
The four phylogenic trees correspond to the descriptions below. The green triangle represents chloroplast proteins and the blue triangles represent cyanobacteria. The white triangles are labeled. Image Source: Sato, N., 2020

Type 1 Tree

Chloroplast enzymes diverged from cyanobacteria (Sato, N., 2020). Proteins, such as galactosyltransferase, are involved in the movement of carbohydrates. Chloroplast proteins separated from the monolithic group (green bacteria and cyanobacteria). But, chloroplasts are organelles, and cyanobacteria are prokaryotes. This tree best illustrates endosymbiosis and chloroplast enzyme divergence (Sato, N., 2020). Likely, their differences are primarily due to the event of endosymbiosis (Sato, N., 2020). 

Type 2 Tree

In the Type 2 Tree, both chloroplast proteins and cyanobacteria are a monolithic group. This group has diverged from green bacteria. Chloroplasts proteins and cyanobacteria have a synapomorphy between them, too. Sato declares that this synapomorphy is the enzyme “sister group.” Sister groups are similar but not identical. 

Type 3 Tree

The Type 3 Tree consists of two separate monolithic groups.  In this case, each group has its own synapomorphy. In other words, there is a synapomorphy between chloroplast and green bacteria chloroplast proteins. The synapomorphy between cyanobacteria and other bacteria equates to the absence of chloroplast enzymes. 

This tree contrasts Type 1 and Type 2 trees since chloroplasts and cyanobacteria are located more distant from each other. Sato hypothesizes that chloroplast proteins originated from homologs, as opposed to cyanobacteria (2020). Therefore, he implies that they have a common ancestor, whose genes remain widely unchanged over time. 

Type 4 Tree

In this phylogenic tree, chloroplasts proteins branch off from the eukaryotic monolithic group. Meanwhile, the prokaryotic group is distinct. If eukaryotes and chloroplast proteins are very closely related, then chloroplast proteins likely developed from eukaryotes (Sato, N., 2020). 


There is a variety of evidence concerning the origins of chloroplasts, depending on which genes scientists are observing. However, scientists found Type 1 in the analysis of ribosomal RNA (rRNA), house-keeping proteins in red algae, and conserved proteins in red algae and Cyanobacteria (Sato, N., 2020). All of these factors support the fact that the chloroplast may have been capable of surviving as a free-living organism, further supporting the endosymbiotic theory. 

This image shows Ribosomal RNA found in both eukaryotic and prokaryotic cells.
A labeled diagram of rRNA aiding in the assembly of the amino acid chain. Image source:

Four models for phylogeny indicate the complexity of chloroplasts and possible endosymbiosis. Some scientists believe that chloroplasts underwent multiple endosymbiosis processes to fully integrate into eukaryotes (Jensen, P. E., & Leister, D., 2014). Regardless of how endosymbiosis occurs, the chloroplast serves the purpose of providing the cell with the necessary chemical compounds that create chemical energy (Jensen, P. E., & Leister, D., 2014). Technical difficulties have limited the study of many proteins involved in photosynthesis (Jensen, P. E., & Leister, D., 2014). Despite these difficulties, scientists have discerned novel retrograde signals.

Novel Retrograde Signals

Retrograde signals have to do with signals from chloroplasts or mitochondria (Jensen, P. E., & Leister, D., 2014). These signals interact with the nucleus to modulate gene expression (Jensen, P. E., & Leister, D., 2014). Many of these signals have not been discovered either due to technical difficulties. But, they do imply another adaptation of these organelles after endosymbiosis (Jensen, P. E., & Leister, D., 2014). Reduction of organelle genomes occurs following endosymbiosis. As a result, organelles must interact with other cellular components, and these organelles proceed from having a mutualistic relationship to a dependent relationship with the rest of the cell. These signals are often a result of metabolic by-products (Jensen, P. E., & Leister, D., 2014). They also show that the evolution of chloroplasts and even mitochondria are dependent upon other cellular components. 

Endosymbiotic Theory and Evolution

Endosymbiosis concerns organelles. Both the mitochondria and chloroplasts carry metabolic processes (respiration and photosynthesis). Scientists often study gene expression with hopes of discovering more about how cells function. However, endosymbiosis highlights the importance of metabolism and its relationship to gene expression. 


Microevolution refers to evolution occurring below the species level (O’Malley, M. A., 2015). Evolution results from mutations in the genome of a species. On a cellular level, silent mutations may occur but might affect complex protein structures needed in either photosynthesis or respiration. O’Malley references instances where endosymbiosis does not have a strong foothold in microbiology. But, its hypothesized importance in eukaryogenesis further supports one of the keystone ideas of evolution: descent with modification. Hence, scientists may apply ideas from endosymbiosis to studying diseases having to do with these organelles. 

Diseases Affecting Mitochondria

Some diseases that affect humans result in mitochondrial dysfunction. Diabetes, cancer, muscular dystrophy, and even Alzheimer’s disease are secondary mitochondrial dysfunction ailments. Notably, one in 5,000 individuals has a genetic dysfunction that affects the mitochondria.

This image shows the comparison of th ebicep muscle in a normal bicep, and in the bicep of someone with muscular dystrophy
The image above compares the biceps of an individual with muscular dystrophy, and an individual without the disorder. Mitochondria influence muscle size. Therefore, without a sufficient mitochondrial volume, muscles experience atrophy. Image source:

Mitochondria were once free-living organisms and still share characteristics with their bacteria and archaea relatives. For example, scientists will sometimes put prokaryotes into a complete medium during instances of metabolic dysfunction. They do this to ensure metabolism has the best conditions to take place. Understanding the optimal setting for mitochondrial activity might be the cure for mitochondrial dysfunction.

Diseases Affecting Chloroplasts

There are not many known diseases that affect the chloroplast directly in plants, but viruses do. However, scientists have found that the chloroplast plays a pivotal role in the synthesis of viral RNA. Chloroplast proteins are known to interact with some viral proteins. In fact, they even attract viral components to the chloroplast, where RNA replication takes place. 

This image shows how viral RNA is replicated in a eukaryotic cell
The diagram above is rather complex. But, the main idea is that a virus depends on the host cell for necessary resources for proliferation. Chloroplasts are one of the organelles able to provide resources for viral RNA replication. Image source:

Chloroplasts, providing a site for viral RNA replication, allow for the creation of bacteriophages. Phages pose a threat to bacteria, and some bacteria are beneficial. Like mitochondria, understanding the metabolism of chloroplasts might be advantageous. If scientists find the optimal conditions for viral RNA replication, they can further research replication prevention methods. Even so, prevention must only affect viral RNA replication without meddling with bacterial metabolism.

Endosymbiotic Theory’s Potential

Scientists face barricades in studying individual organelles because of technological limitations. Consequently, endosymbiosis is still a theory. Research may or may not further validate endosymbiosis with the expansion of scientific knowledge. But, with knowledge gathered thus far, scientists can study the metabolic aspect of disorders and work towards combatting them with treatment besides those aimed at altering the genome.  

Aside from holding great potential, endosymbiosis also reveals how scientific knowledge proceeds. Science is not the truth. Rather, science is the process of obtaining the truth and gathering knowledge surrounding it. Scientists do not possess enough knowledge surrounding the function of chloroplasts and mitochondria before and after endosymbiosis. As a result, the influence that these organelles have on the eukaryotic cell is mostly just hypothesized. As of right now, the use of metabolic knowledge to cure diseases is still novel and untested. But, this hypothesis does have enough ground to stand on before being proven invalid.


Gray M. W., 2017. Lynn Margulis and the endosymbiont hypothesis: 50 years later. Molecular biology of the cell, 28(10), 1285–1287.

Jensen, P. E., & Leister, D., 2014. Chloroplast evolution, structure and functions. F1000prime reports, 6, 40.

Lynch, M., & Marinov, G. K. 2017. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. eLife, 6, e20437.

Martin W, Müller M., 1998. The hydrogen hypothesis for the first eukaryote. Nature. 1998;392:37–41. DOI: 10.1038/32096. 

O’Malley, M. A., 2015. Endosymbiosis and its implications for evolutionary theory. PNAS. 

Sato, N., 2020. Complex origins of chloroplast membranes with photosynthetic machineries: multiple transfers of genes from divergent organisms at different times or a single endosymbiotic event?. J Plant Res 133, 15–33.

Zimorski, V., Ku, C., Martin, W. F., & Gould, S. B., 2014. Endosymbiotic theory for organelle origins, Current Opinion in Microbiology, Volume 22.

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