The Endosymbiotic Theory Of Eukaryotic Cells

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The defining feature of eukaryotic cells is that they contain membrane-bound organelles and a 'true' nucleus. The endosymbiotic theory is based upon the idea that eukaryotic cells evolved in steps beginning with the stable incorporation of chemo-organotrophic and phototrophic symbionts from the domain bacteria. This essay reviewed the evidence that supports this theory. After investigating the molecular, physiological and morphological evidence, it is almost certain that chloroplasts and mitochondria are from the domain bacteria, and that many of the genes required for the survival of these organelles are contained within the nuclear DNA of the eukaryotic cell rather than the organelle's own independent DNA. It is for this reason that I believe that endosymbiosis was the process whereby eukaryotes began to form and evolve. It was found that the genome of a protozoan, Reclinomonas, contained all the protein-coding found in sequenced mitochondrial genomes, providing support for the speculative process of endosymbiotic gene transfer. The hydrogen hypothesis seems to be the most likely scenario for the formation of eukaryotes, which explains the need for compartmentalisation with increasing host genome size to improve efficiency of function throughout the cell, and the chimeric nature of eukaryotes.


Based upon data collected from slow decaying radioactive isotopes, Earth is thought to have formed approximately 4.55 billion years ago. From this time of origin, a continual process of geological and physical change has occurred, which created conditions leading to the origin of life about 4 billion years ago. Life is thought to have undergone the process of evolution, defined as 'DNA sequence change and the inheritance of that change, often under the selective pressures of a changing environment.' (1) Microfossil evidence suggests that unicellular eukaryotes arose on Earth approximately 2 billion years ago, after the development of an oxic environment and the invention of respiratory metabolism in cyanobacteria. This timing infers that the availability of oxygen was a large influence on the biological evolution that led to the emergence of Eukarya. (1)

"The defining characteristic of eukaryotes is the presence of a well-defined nucleus within each cell." (2) Typical eukaryotic cells contain a membrane bound nucleus and organelles enclosed by an outer plasma membrane; these organelles are organised into compartmentalised structures which have their own function(s) within the cell, often working together with other organelles to complete vital biological processes. This compartmentation in cells is essential in organisms as it allows differing compositions of nutrients to exist inside each compartment as opposed to outside, creating perfect conditions for biochemical reactions to occur.(3) The differences between eukaryotes and prokaryotes are shown in Table 1:

Mitochondria are membrane-bound organelles found in the cytoplasm of most eukaryotic cells and are most concentrated in cells associated with active processes, such as muscle cells which constantly require energy for muscle contraction. The two surrounding membranes that encompass a mitochondrion differ in function and composition, creating distinct compartments within the organelle. The outer membrane is regular in appearance and composed of proteins and lipids, in roughly equal measure, whilst the outer membrane contains porin proteins rendering it more permeable. The inner membrane is only freely permeable to oxygen, water and carbon dioxide; it contains many infoldings, or cristae, that protrude into the central matrix space, significantly increasing the surface area and giving it an irregular shape. As can be seen in Figure 1, mitochondria contain ribosomes and have their own genetic material, mitochondrial DNA (mtDNA), separate from the nuclear DNA. (4)

Mitochondria are the principle sites of ATP production- in a process known as oxidative phosphorylation. Products of the Krebs cycle, NADH + H+ and FADH2, are carried forward to the electron transport chain (ETC) and are oxidised to NAD+ and FAD, releasing hydrogen atoms. These hydrogen atoms split to produce protons and electrons, and the electrons are passed down the ETC between electron carriers, losing energy at each level. This energy is utilised by pumping the protons into the intermembranal space causing an electrochemical gradient between the intermembranal space and the mitochondrial matrix. The protons diffuse down the electrochemical gradient through specific channels on the stalked particles of the cristae, where ATPsynthase located at the stalked particles, supplies electrical potential energy to convert ADP and inorganic phosphate to ATP. In mammalian cells, enzymes in the inner mitochondrial membrane and central matrix space carry out the terminal stages of glucose and fatty acid oxidation in the process of ATP synthesis. Mitochondria also play an important role in the regulation of ionised calcium concentration within cells, largely due to their ability to accumulate substantial amounts of calcium. (3)(5)

Chloroplasts are membrane-bound organelles found within photosynthetic eukaryotes. Chloroplasts are surrounded by a double membrane, the outer membrane being regular in appearance whilst the inner membrane contains infoldings to form an interconnected system of disc-shaped sacs named thylakoids. These are often arranged in to stacks called grana. Enclosed within the inner membrane of the chloroplast is a fluid-filled region called the stroma, containing water and the enzymes necessary for the light-independent reactions (the Calvin cycle) in photosynthesis. The thylakoid membrane is the site of the light dependent reactions in photosynthesis, and contains photosynthetic pigments (such as chlorophyll and carotenoids) and electron transport chains. Chloroplasts, like mitochondria, contain ribosomes and their own independent DNA (ctDNA), which is central to the theory of endosymbiosis. The structure of a typical chloroplast is shown by Figure 2:

Radiant energy is trapped by photosynthetic pigments and used to excite electrons in order to produce ATP by photophosphorylation. The light dependent reactions occur in the thylakoid membrane (Photosystem II or P680) and ultimately, these reactions produce the ATP and NADPH required for photosynthesis to continue in the stroma (where Photosystem I or P700 is located). A series of light independent reactions occur within the stroma producing carbohydrates from carbon dioxide and water using ATP and NADPH.

The most supported hypothesis (put forward by Lynn Margulis) for the origin of the eukaryotic cell is that of endosymbiosis which is suitably named as 'symbiosis occurs when two different species benefit from living and working together. When one organism actually lives inside the other it's called endosymbiosis.'(6) The endosymbiosis hypothesis states that 'the modern, or organelle-containing eukaryotic cell evolved in steps through the stable incorporation of chemo-organotrophic and phototrophic symbionts from the domain Bacteria.' In other words, chloroplasts and mitochondria of modern-day eukaryotes arose from the stable incorporation into a second type of cell of a chemoorganotrophic bacterium, which underwent facultative aerobic respiration, and a cyanobacterium, which carried out oxygenic photosynthesis. The beneficial association between the engulfed prokaryote and eukaryote would have given the eukaryote an advantage over neighbouring cells, and the theory is that the prokaryote and eukaryote lost the ability to live independently. (1)

Oxygen was an important factor in endosymbiosis and in the rise of the eukaryotic cell through its production in photosynthesis by the ancestor of the chloroplast and its consumption in energy-producing metabolic processes by the ancestor of the mitochondrion. It is worth noting that eukaryotes underwent rapid evolution, most probably due to their ability to exploit sunlight for energy and the greater yields of energy released by aerobic respiration. Support for the endosymbiosis hypothesis can be found in the physiology and metabolism of mitochondria and chloroplasts, as well as the structure and sequence of their genomes.(1) Similarities between modern-day chloroplasts, mitochondria, and prokaryotes relative to eukaryotes are shown in table 2:

Molecular Evidence

When Margulis proposed the endosymbiotic theory, she predicted that if the organelles really were prokaryotic symbionts, they would contain their own independent DNA. This was proven to be the case in the 1980's for mitochondria and chloroplasts.(7)Furthermore, mitochondrial DNA (mtDNA) was found to have a proportionally higher ratio of guanine-cytosine base pairs than in eukaryotic nuclear DNA, as found in bacteria. These findings are significant as they strongly suggest that mitochondria and chloroplasts are of prokaryotic origin and nature, supporting the possibility that the eukaryotic cell evolved from the stable incorporation of symbionts from the domain Bacteria. Another striking similarity between mitochondria and bacteria is that they both contain 70S ribosomes and contain a comparable order of genes encoding ribosomal proteins a shown in Figure 4:

It is only fair that the molecular problems associated with the endosymbiosis hypothesis that have been put forward are considered. Firstly, mitochondria and chloroplasts can only arise from pre-existing mitochondria and chloroplasts, having lost many essential genes needed for survival. It has been suggested that this is because of the large timespan that the mitochondria/chloroplasts have co-existed. During this time, systems and genes that were no longer needed were either simply deleted or transferred into the host genome. Hence, mitochondria and chloroplasts have lost the ability to live independently over time. This supports the endosymbiotic theory as it provides a reason as to why the ancestors of the chloroplasts and mitochondria were able to survive independently whilst chloroplast and mitochondria are unable to do so now. The study of mitochondrial genomes so far has suggested that mitochondrial genomes actually encode less than 70 of the proteins that mitochondria need to function; most being encoded by the nuclear genome and targeted to mitochondria using protein import machinery that is specific to this organelle.(7) It has been found that the genome of Reclinomonas contains all the protein-coding genes found in all the sequenced mitochondrial genomes: (8)

The importance of Figure 5 is that it shows that the mitochondrial genome no longer contains many of the protein-coding genes, and hence, mitochondria are no longer able to live independently. The mitochondrial endosymbiont is believed to have belonged to the proteobacteria since several genes and proteins still encoded by the mitochondrial genome branch in molecular trees among homologues from this group. Interestingly, mitochondrial proteins such as the 60- and 70-kDa heat shock proteins (Hsp60, Hsp70), also branch amongst proteobacterial homologues, but the genes are encoded by the host nuclear genome.(9) This can be explained by a theory called endosymbiotic gene transfer which states that 'during the course of mitochondrial genome reduction, genes were transferred from the endosymbiont's genome to the host's chromosomes, but the encoded proteins were reimported into the organelle where they originally functioned.' (7) This theory is central to the endosymbiotic theory, as it explains the inability of chloroplasts and mitochondria to live independently even though these organelles are believed to have originated from the domain Bacteria. It is also believed that this gene transfer has provided an essential way in which mitochondrial or chloroplast activity can be regulated. The studies of protists 'raise the possibility that mitochondria originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.' (10) T

This would fit in with the hydrogen hypothesis as described later. A further problem to consider is the extent to which genes were transferred to the cell nucleus. Why did some genes remain in the cytoplasmic organelles? This question has been addressed by the Co-location for Redox Regulation (CoRR) hypothesis, which states that the location of genetic information in cytoplasmic organelles permits regulation of its expression by the reduction-oxidation ('redox') state of its gene products. Therefore, evolution by natural selection would have favoured mitochondrial or chloroplast cells that had deleted or transferred some genes to the host genome but had kept those that were still beneficial in the regulation of the organelle's activity. (11)

Physiological Evidence

Evidence for the endosymbiosis theory can be found in the physiology of mitochondria and chloroplasts. For example, both mitochondria and chloroplasts have their own protein-synthesising machinery which closely resembles that of Bacteria rather than that of Eukaryotes. Ribosome function in mitochondria and chloroplasts are inhibited by the same antibiotics that inhibit ribosome function in free-living bacteria. Hence, it is no surprise that both these organelles contain 70S ribosomes typical of prokaryotic cells, and show 16S ribosomal RNA gene sequences, a characteristic of certain Bacteria such as Escherichia coli.(1) For example, human mitochondrial ribosomes can be affected by chloramphenicol (an antibiotic used to inhibit protein synthesis), further evidence that mitochondria are likely to be of bacterial origin. Chloramphenicol is a relatively simple molecule containing a nitrobenzene ring responsible for some of the toxicity problems associated with the drug:

Chloramphenicol inhibits protein synthesis due to its high affinity for the large (50S) ribosomal subunit, which when bound to chloramphenicol, blocks the action of peptidyl transferase, preventing peptide bond synthesis. It has also been discovered that chloramphenicol prevents the maturation of the 30S ribosomal subunits, decreasing the number of competent subunits and significantly decreasing the proportion of mitochondrial ribonucleoprotein present as monomers. (12) Also, the antibiotic rifampicin which inhibits the RNA polymerase of Bacteria has been found to inhibit the RNA polymerase within bacteria. Proteins of chloroplast or mitochondrion origin, like bacteria, always use N-formylmethionine as their initiating amino acid of their transcript.(13) Mitochondria replicate, like bacteria, only by the process of binary fission inferring that mitochondria did indeed originate from prokaryotes. The completion of the genome sequence of the cyanobacterium Synechocystis, has provided evidence for the origin of chloroplast translocation apparatus. Just as the endosymbiosis theory predicts, analysis of this sequence showed that three key translocation components within chloroplasts, Toc75, Tic22 and Tic20, evolved from existing proteins within the cyanobacterial genome.(14)Mitochondria and chloroplasts have remarkably similar mechanisms by which ATP is produced. These ATP-generating pathways often include electron transport chains and proton pumps, similar to that found in prokaryotic energy production mechanisms.

One of the most recent problems with the endosymbiosis theory is found within the physiology of mitochondria. 'Mounting evidence suggests that key components of the mitochondrial transcription and replication apparatus are derived from the T-odd lineage of bacteriophage rather than from an α-Proteobacterium, as the endosymbiont hypothesis would predict.'(15) It has been discovered that three of the essential elements of the replication and transcription apparatus; the RNA polymerase, the replicative primase-helicase and the DNA polymerase do not resemble those of eubacteria as predicted by the symbiosis theory, but instead appears to resemble proteins encoded by T-odd bacteriophages. However, this does not disprove the theory of endosymbiosis as it is conceivable that numerous mitochondrial genes were acquired together from an ancestor of T-odd phage early in the formation of the eukaryotic cell, at the time when the mitochondrial symbiont was incorporated. (15)

Morphological Evidence

Another characteristic that further supports the hypothesis is that mitochondria and chloroplasts contain small amounts of DNA that is different from that of the cell nucleus which is arranged in a covalently closed, circular structure, with no associated histones, typical of Bacteria. Mitochondria are surrounded by two membranes, separated by the inter-membranal space and each with a different composition. Mitochondrial membranes more closely resemble membranes found in Gram-negative bacteria in terms of lipid composition than eukaryotic membranes. (16) The inner-membrane infoldings in the mitochondria lends more credibility to the endosymbiosis theory as the cristae "are adaptations that increase the surface area of oxidative enzymes, evolutionary analogues to the mesosomal membranes of many prokaryotes" (16)Further evidence that mitochondria and chloroplasts are of a prokaryotic origin is the lack of cholesterol in their membranes. This is significant because it is an essential structural component in many eukaryotic membranes, mainly in mammalian cell membrane, but it almost completely absent amongst prokaryotes.

Another problem is that recent genetic analysis of small eukaryotes that lack many characteristics that are associated with eukaryotic cells, most importantly mitochondria, show that they all still retain genes involved in the synthesis of mitochondrial proteins. In 1983, the taxon Archezoa was proposed to unite this group of odd eukaryotes, and the belief was that these cells had diverged from other eukaryotes before these characteristics evolved and hence represented primitive eukaryotic lineages. Before the recent genetic breakthrough that shows that these eukaryotes contain genes involved in mitochondrial protein synthesis, molecular work supported their primitive status, as they consistently fell deep into the branches of eukaryotic trees. This recent genetic analysis implies that all these eukaryotes once had mitochondria, suggesting that they evolved after the mitochondrial symbiosis. There is also the question of how the eukaryotic cell arose, including the nature and properties of the cell that acquired mitochondria and later chloroplasts, and how the nuclear membrane was formed which touches upon the compatmentalisation within cells and its importance in the functioning of the eukaryotic cell. (7)

Formation of the eukaryotic cell

There have been two hypotheses put forward to explain how the eukaryotic cell arose. One states that eukaryotes started as a nucleus-bearing lineage that later acquired the bacterial ancestor of the mitochondrion and the cyanobacterial ancestor of the chloroplast by the process of endosymbiosis. This nucleated line then diverged into the lineages giving rise to animals and plants. It is thought that the nucleus arose spontaneously in an early cell. One possible cause for the spontaneous formation of the nucleus is that it arose in response to the increasing genome size of early eukaryotes. (1)

The second hypothesis, also known as the hydrogen hypothesis, states that the bacterial ancestor of the mitochondrion was taken up by a member of the Archaea via endosymbiosis, and from this association, the nucleus later emerged, followed by a later acquisition of the cyanobacterial ancestor of the chloroplast. The main difference between these two hypotheses is the position of the mitochondrion relative to the formation of the nucleus in time and hence on the universal phylogenetic tree. The hydrogen hypothesis put forward by William F. Martin and Miklos Muller in 1998, proposes that the eukaryotic cell arose from a symbiotic association of an anaerobic, hydrogen dependent, autotrophic archaebacterium (the host) with a hydrogen producing, oxygen consuming eubacterium (the symbiont), which released molecular hydrogen as a waste product of anaerobic heterotrophic metabolism. (17) The dependence of the host upon the molecular hydrogen as an energy source, produced as a waste product by the symbiont is thought to be what lead to the association. In this scenario, the nucleus arose following the formation of this stable association between these two kinds of cells, and genes involved in lipid synthesis were transferred from the symbiont to the host chromosome. This may have lead to the synthesis of bacterial (symbiont) lipids by the host, eventually leading to the creation of an internal membrane system, the endoplasmic reticulum and the early stages of a eukaryotic nucleus. As the size of the host genome increased with time, changes were made to maximise the efficiency of replication and gene expression via the process of evolution. Hence, over time, this kind of cell compartmentalised and sequestered the genetic coding information within a protected membrane away from the cytoplasm. The formation of a mitochondrion-containing nucleated cell line was complete, which then later acquired chloroplasts by endosymbiosis. The hydrogen hypothesis has explains the observation that eukaryotes are of chimeric nature, containing attributes of both Bacteria and Archaea. (1)


In summary, molecular, physiological and morphological evidence can be found to support the endosymbiosis theory put forward by Lynn Margulis. Most compelling of which is the numerous similarities between organelles such as chloroplasts and mitochondria with prokaryotes, coupled with the inability of the organelles to live independently despite having their own independent DNA due to most of the genes required for the survival of the organelle being stored in the nuclear DNA of the host. The importance of this should not be underestimated, as it does all but prove that the ancestors of mitochondria and chloroplasts were of a prokaryotic origin and thus were once able to live independently. Therefore, this does lend credibility to the endosymbiosis theory as the symbionts that were allegedly incorporated were likely to have been from the domain bacteria, and that something must have occurred which stopped the symbionts being able to live independently, an event which many scientists now believe to be the process of endosymbiotic gene transfer. The hydrogen hypothesis appears to be the likely scenario for how the eukaryotic cell evolved, as it explains the formation of the nucleus as being a response to the growing size of the nuclear genome of the host, which would have maximised efficiency of gene expression. Endosymbiosis also explains why the eukaryotic cell appears to be of a chimeric nature; containing attributes of Archaea (e.g. similar transcription and translation apparatus) and Bacteria (e.g. contain same type of lipids).