A essay of around 3000 words, introducing the endosymbiotic theory and the theories for & against it

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Name: JohnathanTsui Wei Yau
Course: Microbiology and Virology
Student number: 1222880
Date:10-04-2013
Word count: 2964
Extended essay: Reviewing the evidence for the Endosymbiotic theory-
the modern, or organelle containing eukaryotic cell evolved in steps
through the stable incorporation of chemo-organotrophic and
phototrophic symbionts from the domain Bacteria
Abstract (100 words max): An introduction to the Endosymbiotic theory is first given to
provide an overview of the content of discussion, more specifically the evidence and theories for and
against it. The next two sections serve to describe the two main alternative theories as opposed to the
SET, preventing the assumption that it is the most validated theory. Next section that ensues discusses
mainly evidences which support the SET,it is further divided into two sub-sections using two of the
main eukaryotic organelles concerned- mitochondria and chloroplasts. Finally, a conclusion regarding
all the surrounding arguments discussed is given.

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A brief introduction to Endosymbiotic theory
To put it bluntly, Endosymbiotic theory (or SET, Serial Endosymbiosis Theory) is a theory that tries to
explain the evolutionary origin of organelles in modern day eukaryotic cells. “As early as 1883, A.F.W
Schimper proposed that the chloroplasts of plants were cyanobacteria that lived symbiotically inside
plant cells…..Early scientists such as Ivan Wallin were convinced that mitochondria were bacteria that
lived inside cells.” (Paracer and Ahmadjian 81) It was first revitalized and put forth in the 1960’s by
Lynn Margulis, a biologist from Boston University, and published in her book “Symbiosis in Cell
Evolution” in 1981. It proposes that organelles residing in eukaryotic cells, most notably mitochondria
and chloroplasts (possibly peroxisomes, hydrogenosomes, etc other membrane bound organelles),
originated from the endocytosis of aerobic eubacteria and cyanobacteria (respectively) by anaerobic
prokaryotic host cells (archaebacteria). Unable to digest the engulfed bacteria, they developed a
symbiotic relationship (where two species gain mutual benefits by living alongside each other) over
billions of years, hence the name “endosymbiosis”. The prokaryotes that were once unable to utilize
oxygen began to acquire abilities to carry out aerobic respirations and eventually photosynthetic
reactions by successive endosymbiosis events. As time progressed, the engulfed bacteria transferred
some genes to the host cell’s genome, resulting in the permanent interdependence on each other’s
metabolic activities. Eventually, they developed into some of the known organelles such as
mitochondria and chloroplasts.

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As a boldly proposed theory, the SET was questioned by the scientific community throughout the 19th
and 20th
century as there is no way to support it with experimental results. However, the advancement
of scientific knowledge and technologies in recent years allows the structural, molecular and
biochemical scrutiny of eukaryotic organelles to construct probable backup on the SET. Some of these
evidences include the fact that both mitochondria and chloroplasts possess their own circular DNA
(though not all in mitochondria), which strongly resembles prokaryotic cells; the fact that these
organelles synthesize their own proteins and perform binary fission is also a powerful evidence.
Some of the evidences which hint the validity of SET will be examined in the following sections of this
essay, while arguments that the SET cannot be established will also be examined in order to provide an
objective, bird eyes’ view on this particular subject. Before this, however, some of the other theories
and hypothesis regarding the rise of eukaryotic organelles will also be mentioned for the sake of
balancing alternative views on this matter.

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Autogenous Theory
Figure 1- this is a simple illustration of how infoldings of an ancestral prokaryote can result in single membrane
organelles such as ER and nucleus, which leads to further compartmentalization of plasmids within these
invaginations that results in the appearance of organelles like mitochondria
The autogenous theory proposes that organelles such as nucleus, endoplasmic reticulum, Golgi
apparatus, vacuoles and lysosomes first “evolved from elaborations of the cell and other internal
membranes” (Paracer and Ahmadjian 80), or in other words progressive compartmentalization as seen
in figure 1. These single membrane organelles arise from the infoldings of a prokaryotic ancestor cell’s
plasma membrane (Gwu.edu), and organelles such as mitochondria and chloroplasts successively
evolved after the appearance of a prototype eukaryote by compartmentalization of plasmids within the
invaginations of the cell membrane (Gwu.edu). The common features found between mitochondria &
chloroplasts and eubacteria as proposed in SET might be explained by mosaic evolution, where “the
components in the compartment evolved more slowly than other parts of the cell” (Gwu.edu), thus
explaining why they possess some of the molecular and structural similarities to a prokaryotic cell. The

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fact that they have double membrane can also be explained by possible, secondary invaginations of the
plasma membrane.
The Hydrogen Hypothesis
Figure 2- On the left hand side, type II amitochondriate eukaryote resembles the anaerobic proteobacterium that
also utilizes hydrogenosome to generate ATP, with hydrogen, carbon dioxide and acetate discarded as waste
products; this proposed endosymbiont is compared to a eukaryote with mitochondria as seen on the right

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Figure 3- this is a simple illustration of how the archaen (methanogen), which takes in hydrogen, carbon dioxide
and acetate to produce ATP with methane discarded as waste products, engulfed the proteobacterium (hydrogen-
producing symbiont) over time
In short, the hydrogen hypothesis “is based on the symbiosis between an alpha proteobacterium and an
archaean (methanogen)” (Paracer and Ahmadjian 81). In aerobic cell respiration performed by
mitochondria (following glycolysis), pyruvate is decarboxylated into acetyl-CoA by the PDF (Pyruvate
dehydrogenase complex), which is then oxidized in the citric acid cycle into NADH, CO2 and water,
together with 36 mol of ATP for each mol of glucose consumed. The proteobacterium involved in the
symbiosis performed respiration similar to an anaerobic amitochondriate eukaryote with
hydrogenosome, where pyruvate is converted into acetate, CO2 and reduced ferredoxin by the pyruvate
ferrodoxinoxidoreductase (PFO). The reduced ferredoxin is reoxidized by hydrogenase, producing ATP
and hydrogen, hydrogen is discharged with carbon dioxide and acetate as waste products, as seen in
figure 2. On the other hand, the archaean involved are methanogens- obligate anaerobe that uses
hydrogen and carbon dioxide to produce ATP (Acetyl-CoA pathway) and methane (Methanogenesis),

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with methane discarded as waste products. This ensures that symbiosis took place as mutual benefits
between these two organisms were guaranteed. The archaean became the host with the proteobacterium
as the endosymbiont, as depicted in figure 3. Eventually, the host became dependent on the
proteobacterium and genetic transfer occur from the proteobacterium to the host , “the host provided
the membrane proteins for the import of substrates and enzymes for glycolysis, and ATP production
began under anaerobic conditions” (Paracer and Ahmadjian 83). As time progressed, the archaean host
began to utilize more complex and organic molecules instead of hydrogen and carbon dioxide.
Evidences supporting the Endosymbiotic Theory
In the following sections, information that point towards the SET will be discussed, and will be divided
between the two major eukaryotic organelles that are often considered- mitochondria and chloroplasts.

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Mitochondria
Figure 4- A 3D cross-sectional view of a mitochondrion, which contains its own circular mitochondrial DNA,
ribosomes (note that they are 70S), ATP synthase and double membrane. It is of no surprise that some speculate its
origin from a prokaryotic cell, which also possesses a circular DNA molecule and ribosomes of the same size
One of the main claims that mitochondria might have originated from an ancestral proteobacterium is
that a mitochondrion possesses its own single, circular DNA molecule that is not associated with
histones, proteins that participate in the organization and wrapping of DNA in eukaryotic cells. In
human mitochondria, it consists of 37 genes (Endosymbiosis and the Origin of Domain
Eukaryotafossilmuseum.net)“16,569 base pairs of DNA in a closed circle which encodes 2 rRNA
molecules, 22 tRNA molecules and 13 polypeptides, with these polypeptides constructing protein
complexes such as NADH dehydrogenase complex, ATP synthase, cytochrome c oxidase and
cytochrome b in the inner mitochondrial membrane” (Endosymbiosis and The Origin of Eukaryotes

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users.rcn.com). This indeed bears an extremely close resemblance to a prokaryote, which also has its
own circular DNA that is free of histones. However, mitochondrial DNA in different organism do not
share the same size, with “two or three times more genome in plant mitochondria than in animal
mitochondria” and “much of the plant mitochondrial DNA consists of noncoding sequences known as
introns” (Paracer and Ahmadjian 85). As prokaryotic DNA is not consisted of introns, despite the
striking similarity between the molecular features of mitochondria and prokaryotes, one cannot insist
that mitochondria definitely derived from ancestral eubacteria. By studying the mitochondria of fungus,
it was found that the tRNA sequences are not similar to either prokaryotes or most eukaryotes (Paracer
and Ahmadjian 85). Also, mitochondrial mRNA “have intervening sequences, or introns, along with
post-transcriptional processing” (Paracer and Ahmadjian 85) which is again not a feature spotted in
prokaryotes but only in eukaryotes. However, one can still argue in favor of the SET that mitochondrial
genome consists of introns because of the transfer of genes between the host and the involved
endosymbiont, which results in changes in the genetic makeup of the proto-mitochondrion.
Another piece of evidence pertaining to this matter is that mitochondria have 70S ribosomes that are
also found in prokaryotes but not in eukaryotes, and they have their own unique protein-synthesizing
mechanism that again relates to prokaryotic cells. Antibiotics such as streptomycin block protein
synthesis in bacteria but not in eukaryotic cells, and they too block protein synthesis in mitochondria;
similarly, rifampicin inhibits both the RNA polymerase of bacteria and mitochondria but not that of
eukaryotes (Endosymbiosis and The Origin of Eukaryotes users.rcn.com). On the other hand, inhibitors

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such as diphtheria toxin act on protein synthesis of eukaryotes but not that of bacteria or mitochondria
Endosymbiosis and The Origin of Eukaryotes users.rcn.com). The fact that the translation machinery in
mitochondria bears such likeness to that found in prokaryotes does help to validate the SET, but not
fully justify it as it is not flawless. Pertaining to this evidence it is possible to counter it with the
autogenous theory, which argues that mitochondria resemble prokaryotes because of mosaic evolution,
where components within the compartments formed by invaginations of an ancestral prokaryotic cell’s
plasma membrane evolved much slower than the other parts.
Figure 5- Electron microscope images of Rhodopseudomonas (left) and R. prowazekii (right); Rhodopseudomonas
is a gram-negative bacteria that can display four modes of metabolism: photoheterotrophic, photoautotrophic,
chemoheterotrophic and chemoautotrophic; R. prowazekii is also a gram-negative, intracellular (obligate) and
aerobic alpha proteobacteria that is the causative agent of typhus; they are both genetically and molecularly related
to mitochondria
Perhaps the most solid evidence that supports the SET, “the sequences of cytochromes, ferredoxin, and
5S rRNA in mitochondria are similar to those of photosynthetic prokaryotes such as
Rhodopseudomonas” and by “sequencing rRNA from mitochondria of fungi, mice and humans, from

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nuclei of animals, yeast, and corn chloroplasts, and from E.coli that the greatest similarity in conserved
sequences was between mitochondria and prokaryotes” (Paracer and Ahmadjian 85). Molecular
sequencing also displays that proteobacteria are the closest modern day relatives to mitochondria, as
“sequence data suggest that all extant mitochondria are derived from an ancestor of R. prowazekii
(gram-negative proteobacteria) as the result of a single endosymbiotic event (2% of the protein-coding
genes inE.coli are found in all examined mitochondria).” (Berg, Tymoczko and Stryer 546)
Another interesting evidence to note is that mitochondria is involved in the intrinsic apoptosis pathway,
which is “initiated by the formation of the cytosolic apoptosome composed of Apaf-1 (protease),
procaspase 9, and the cytochrome c released from mitochondria” (Jeong and Seol, “The role of
mitochondria in apoptosis”) in response to apoptotic signals. This reflects the interdependence
displayed between the host and endosymbiont in ancient times after endosymbiosis had taken place for
billions of years, as a result of gene transfer between the two.

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Chloroplasts
Figure 6- A two dimensional cross-section view of a chloroplast, which, similar to mitochondria, also possesses its
single circular loop of DNA, 70S ribosomes and double membrane; however, they are unique in the sense that they
have these extensive system of membranous sacs called thylakoids that actively engage in light-dependent
reactions by containing photosynthetic pigments
Chloroplasts, like mitochondria, also have their own unique single, circular DNA. There are 128 genes
that include “duplicate genes encoding each of the four subunits of the rRNA, 37 genes encoding tRNA,
4 genes encoding parts of the subunits of RNA polymerase, one gene encoding the large subunit of the
enzyme RUBISCO (small subunit encoded by nuclear genome), 9 genes for components of
photosystems I and II, 6 genes for parts of the ATP synthase and the rest of the genes for 19 of the 60
proteins used to construct ribosome” (Endosymbiosis and The Origin of Eukaryotes users.rcn.com).
Like mitochondria, this bears a resemblance to prokaryotic cells. Furthermore, the fact that chloroplasts
rely on nuclear genes to encode their structural proteins (for instance the small subunit of the enzyme
RUBISCO used in the Calvin Cycle) translated in the cytosol, which are then transported into the

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chloroplasts supports the interdependence that had resulted from billions of years of endosymbiosis
where gene transfer took place and stripped the endosymbiont of the ability to live on its own. “Plastids
(major double membrane organelles in plants that specialize in the storage and assembly of compounds
required by cells) typically contain some 60-100 genes, compared to cyanobacteria that have some
1500 genes.” (Endosymbiosis and the Origin of Domain Eukaryotafossilmuseum.net) This again
demonstrates the gleaming possibility of the endosymbiont’s gene transfer to its host over the course of
endosymbiosis.
Another evidence which supports chloroplasts originated as cyanobacteria that were engulfed by
prokaryotic host cell capable of phagocytosis is that chloroplasts have double phospholipid bilayers.
“The inner membrane represents the plasma membrane of the original prokaryotic symbiont, and the
outer membrane either represents the vacuolar membrane formed by the host around the symbiont or is
the remnant outer membrane of the Gram-negative cyanobacterium that was the endosymbiont.”
(Paracer and Ahmadjian 85) Other plastids such as chromoplasts and leucoplasts could have been
derived from secondary endosymbiosis, where heterotrophic eukaryotes proceeded to engulf other
photosynthetic eukaryotes. For instance, “a group of unicellular, motile algae called cryptomonads
appear to be the evolutionary outcome of a nonphotosynthetic eukaryotic flagellate engulfing a red alga
by endocytosis.” (Endosymbiosis and The Origin of Eukaryotes users.rcn.com); perhaps more
specifically, Paramecium bursaria, a unicellular eukaryote, engulfs green algae named zoochlorella
and develops a symbiotic relationship with it instead of digesting it. Zoochlorella provides

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P.bursariawith the ability to photosynthesize sugar, while they “extract nourishment from the host
when it is well fed and when they are deprived of light” and are “situated within individual vacuoles
and these alga-vacuole complexes grow and divide at a rate compatible with that of the paramecium.”
(Karakashian, “Symbiosis in Paramecium. Bursaria”) These are solid living examples of
endosymbiosis that provide insights as to the rise of eukaryotic cells. However, it is still possible to
argue that plastids like chloroplasts arise as a result of secondary and even further invaginations of the
ancestral prokaryotic cell’s plasma membrane, resulting in the phenomenon that the “chloroplasts of
Euglena have three outer membranes, and those of brown algae and diatoms are surrounded by four
membranes” (Paracer and Ahmadjian 85).
Chloroplasts are very similar to mitochondria in the sense that they also possess 70S ribosomes found
commonly in prokaryotes, and their own protein-synthesizing mechanism. For instance, Methionine is
always the first amino acid to be translated along the mRNA transcript; antibiotics such as streptomycin
prevents protein synthesis in chloroplasts just as it is in bacteria and inhibitors such as diphtheria toxin
has no effect on protein synthesis unlike eukaryotes (Endosymbiosis and The Origin of Eukaryotes
users.rcn.com). Just as it was mentioned under the “mitochondria” section, one can argue that this does
not support the SET by applying the autogenous theory, which simply considers the prokaryotic
molecular features of mitochondria and chloroplasts as a result of mosaic evolution.

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Perhaps the strongest piece of evidence for the SET regarding chloroplasts is from data collected from
molecular sequencing, such as “DNA-RNA hybridization of chloroplasts, nucleocytoplasm, and
cyanobacteria and sequencing of plastocyanin, ferredoxin, and cytochrome c….have indicated a close
relationship between chloroplasts and blue-green prokaryotes.” (Paracer and Ahmadjian 86) More
importantly, the 5S and 16S sequences of chloroplast rRNA is much similar to that of cyanobacteria
than that of eukaryotes (Paracer and Ahmadjian 86).
Conclusion and Discussion- Is the Serial Endosymbiotic Theory entirely credible?
The information and evidences presented regarding the SET are largely overwhelming due to the
breadth of this topic, and the sections above barely provided a glimpse of arguments supporting and
against this evolutionary theory. The fact that both mitochondria and chloroplasts greatly resemble
prokaryotes both morphologically and molecularly, as they both possess double phospholipid bilayers,
circular DNA molecule, 70S ribosomes and DNA/RNA sequences similar to prokaryotes, increases the
credibility of the endosymbiotic theory. These organelles are potentially the descendants of engulfed
proteobacteria and cyanobacteria that goes back to billions of years ago. The sequencing of proteins
and nucleic acids had substantially proven the genetic link of these organelles to their ancestral cells;
also, there are living organisms such as Paramecium bursaria that can be presented as living proof of
the possibility of endosymbiosis as a way of mutually benefitting both the host and the endosymbiont.

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However, the SET is not without its flaws: “All evolutionary theories must offer an explanation in
mechanistic terms of how it should or could have happened in order to be tested.” (Albert de Roos,“A
critique on the endosymbiotic theory for the origin of mitochondria”) The exact mechanisms of how
the genetic transfer from the endosymbiont to the host occurred, how organelles like mitochondria and
chloroplasts acquired their double phospholipid membranes, how the interdepence between the two
evolved are not explained in this vaguely defined theory. The fact that endosymbiotic theory claims
mitochondria derived from the endocytosis of aerobic proteobacteria by anaerobic archaebacteria
presents a problem, as the host cell clearly could not tolerate any oxygen whilst the endosymbiont
require oxygen to carry out aerobic respiration. There would also be a competition for energy resources
as the endosymbiont requires ATP and would not easily transport them to the host cell. There is also the
problem that “the extensive gene transfer that is needed in the endosymbiotic theory would wreak
havoc in a complex genome since frequent insertion of random pieces of endosymbiont’s DNA would
disrupt existing functions…the endosymbiotic theory is in contrast with the concept of gradualism that
forms the basis of modern evolutionary theory.” (Albert de Roos,“A critique on the endosymbiotic
theory for the origin of mitochondria”) Pertaining to the evidence that mitochondria have circular DNA
similar to that of bacteria, linear mitochondrial DNA molecules exist with “eukaryotic telomeres”.
(Albert de Roos,“A critique on the endosymbiotic theory for the origin of mitochondria”) Although
genetic sequencing supports that mitochondria have a monophyletic origin from proteobacteria, “recent
studies of protists…indicate that the mitochondrion arose in a common ancestor of all extant
eukaryotes and raise the possibility that this organelle originated at essentially the same time as the

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nuclear component of the eukaryotic cell rather than in a separate, subsequent event.” (Gray, Burger
and Lang, “Mitochondrial evolution”) In other words, the autogenous theory seems to explain the rise
of mitochondria better as it claims that organelles form from invaginations of an ancestral prokaryotic
cell’s plasma membrane. Speaking of the autogenous theory, it also appears to be more favorable as the
evolution of eukaryotic organelles could be “driven by the advantages to sequester metabolic activity in
specialized compartments.” (Albert de Roos,“A critique on the endosymbiotic theory for the origin of
mitochondria”) The specific roles of the different organelles could have been based on the existing
metabolic functionalities, which were expanded and amplified gradually over time. In an addition, “the
mitochondrial genes could be derived from transposable elements, plastids or viruses and could come
from either the nuclear genome or a bacterial genome.” (Albert de Roos,“A critique on the
endosymbiotic theory for the origin of mitochondria”)
In short, the true evolutionary origins of eukaryotic organelles is still undetermined due to the vast
amount of time scientists are covering and the lack of substantial proof as to how every bit of the
mechanism worked, with no way to experimentally testify. Although the SET offers a probable theory
of endosymbiosis coupled by evolution that is backed by modern molecular data and observation, there
are still a lot of questions unanswered and missing links undiscovered. Other viable options such as
autogenous theory present a simpler and more direct suggestion as to the rise of eukaryotic organelles,
and while they are not without faults these alternative theories should be considered before the final
answer is sealed.

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