The oldest eukaryotic fossil is approximately 1.5 billion years old. The origin of the eukaryotes must have appeared before because the fossil is of a relative complex single-celled organism.

Biologists are almost certain that eukaryotes evolved from prokaryotes because:

1. Both use RNA and DNA are the genetic material

2. Both use the same 20 amino acids

3. Both have ribosomes and DNA and RNA

4. Both have a lipid bilayer cell membrane.

5. Both use L amino acids and D sugars

1. microtubules (composed of the protein tubulin) and actin molecules-

• cytoskeleton for support or intracellular transport.-
  
• flagella (or cilia)

2. DNA in chromosomes (intertwined with histone protein)

3. membrane-bound organelles.

There is no fossil record recording the evolution of the eukaryotes. So most hypotheses have been inferred from studying the biology of modern organisms.

Perhaps the most significant difference between prokaryotic and eukaryotic cells, if we want to understand the origin of the later, is that prokaryotes are inclosed in a rigid cell wall, whereas eukaryotes usually are not and can change their cell shape easily.

The absence of the cell wall does, however, mean that the eukaryote needs some other way of supporting and strengthening the cell surface (a wall-less naked cell membrane is very fragile). Eukaryotes have evolved a complex cytoskeleton consisting of two classes of molecules:

1. Actin filaments - resist pulling forces and convert chemical activity into mechanical motion. This is an endothelial cell stained to show actin filaments in the cytoskeleton:

Cytosis is the ability of membranes to grow and fuse and it allows cells to both secrete substances efficiently (exocytosis) and to bring them into the cell more efficiently (phagocytosis).

Following the loss of a cell wall and the apearance of the cytoskeleton, there are two different stories to tell about the origin of eukaryotes, one for the origin of organelles such as mitochondria and chloroplasts, and another for the origin of the of other parts of the cell. Cytosis may explain the former:

According to this theory:
€a prokaryotic cell capable of engulfing other prokaryotes, engulfed aerobic bacteria.

-Rather than digesting them, the bacteria remain, as symbionts, benefiting the host cell by removing harmful O2 and helping in the production of ATP.

- As interdependence between the aerobic bacterium and the host cell grows, the bacterium becomes the mitochondrion.

- Some of these cells also engulf and keep blue-green algal cells which become chloroplasts.


Endosymbioic origin of mitochondria and chloroplasts is an old idea:

The physical appearance of chloroplasts and mitochondria as observed by light microscopy was the justification used by Schimpler (1883) to make the first explicit proposal of symbiotic, bacterial origin of plastids, while Walin (1922) did the same for mitochondria.

These observations appeared to be supported later by electron microscopy when it was discovered that both organelles were surrounded by two membranes - the inner one supposedly belonging to the symbiont and the outer one a remnant of the membrane used by the host cell to engulf the symbiont.

Today, the endosymbiotic theory is most closely associated with the work of Lynn Margulis. She has further added to the hypothesis in two ways:

1. She has suggested that the eukaryotic flagellum arose from an ectosymbiotic spirochete bacterium. Confirmed evidence for this is rather slim: spirochetes are known to attach to the surface of a protozoan (Myxotricha paradoxa) that lives in the digestive tract of termites and to provide it with locomotion. (Spirochetes do not contain microtubules and flagella do not have their own strand of DNA as Margulis has claimed).

2. No prokaryote living today has ever been known to have another prokaryote living symbiotically inside of it. Is symbiosis in prokaryotes even possible? Margulis has therefore suggested that a prokaryote first developed a membrane around its DNA to form a "protoeukaryote" without anyother membrane-bound organelles. This protoeukaryote then is the organisms that serves as the host for the bacteria which eventually become mitochondria, chloroplasts and flagella.


The endosymbiotic origin of mitochondria and chloroplasts is widely believed because of the many similarities between prokaryotes and these organelles:



1. Mitochondria and chloroplasts are similar in size and shape to prokaryotes

2. Mitochondria and chloroplasts have their own DNA that lack histone proteins, that is circular, and is attached to the inner membrane as is the DNA of prokaryotes

3. Organellar ribosomes are more similar in size to prokaryotic ribosomes

4. Mitochondria and chloroplasts divide by fission, not mitosis.

5. Mitochondria arise from preexisting mitochondria; chloroplasts arise from preexisting chloroplasts (they are not manufactured through the direction of nuclear genes).

6. Outer membrane or chloroplasts or mitochondria would have been synthesized by the original "host" cell and used to engulf the endosymbiotic bacteria that became the mitochondria. The outer membrane has structural and chemical similarities to the eukaryote cell membrane.


Note: similar evidence to support the idea that spirochaete bacteria gave rise to flagella does not exist. Tubulin (the primary component of microtubules) has not been found in any prokaryote, and DNA has never been found in flagella. Most evolutionary biologists reject the idea that flagella originated by symbiosis.

Endosymbiosis is undoubtedly a fascinating concept and, at first glance, the evidence appears to support it as the mechanism for the evolution of chloroplasts and mitochondria. But it really isn't very good evidence - it is questionable on two counts.

1. It supports the alternative hypothesis equally well (in fact some of the features of mitochondria may be explained better by the alternative hypothesis).

2. It is the wrong sort of evidence because none of these data have been shown to be synapomorphies between prokaryotes and organelles.


Alternative Hypothesis - Autogenous
According to the autogenous model, the eukaryotes arose directly from a single prokaryote ancestor by compartmentalization of functions brought about by infoldings of the prokaryote plasma membrane. This model is usually accepted for the endoplasmic reticulum, golgi, and the nuclear membrane, and of organelles enclosed by a single membrane (such as lysosomes). According to the autogenous hypothesis, mitochondria and chloroplasts have evolved within the protoeukaryote cell by compartmentalizing plasmids (vesicles of DNA) within a pinched off invagination of the cell membrane.

Similarities between mitochondria or chloroplasts and eubacteria can be accounted for by mosaic evolution in which the components in the compartment evolve more slowly than other parts of the cell, and thus retain many eubacterial features. Mitochondria or chloroplasts may have acquired their double-membrane status by secondary invagination or more elaborate folding of membranes.

Other problems with the "Evidence" for endosymbiosis

1. Organelles are the same size and shape are bacteria - It is possible to find some chloroplasts the same size and shape as some bacteria, but the range in size and shape is so great we cannot rule out that they are similar just by chance.

Many mitochondria actually have a reticulated structure. Mitochondrial profiles seen in sections with the electron microscope only appear to be the same size and shape as bacteria but these are just the branches of a large reticular structure.

2. DNA in a circular loop. The DNA of organelles is much more like that of a plasmid (easily relaxed, super coiled and doubly covalently linked) than like the DNA of bacteria.

Furthermore, in mitochondria, the DNA is not always circular. In the mitochondria of ciliates (e.g., Paramecium) it is linear.

In kinetoplastids (trypanosomes and close relatives) it consists of closely-linked minicircles (No bacterium has DNA like that!). Furthermore, most of the mitochondrial genes can also be found in the nucleus (endosymbiosis proponents explain this as leaping genes).

3. Similar sized ribosomes. The size of ribosomes in organelles varies among eukaryotes (60-80S) and while that does overlap with prokaryotic ribosomes (70S for eubacteria) it also overlaps with the cytoplasmic ribosomes of eukaryotes (78-80S).


Search for Synapomorphies --

The alternative theories for the evolution of eukaryotes make quite different predictions about the similarities that one might expect to find among eubacterial, nuclear, and organellar genomes. The autogenous origin hypothesis predicts that plastid and mitochondrial genomes should share more synapomorphies to nuclear genomes than to prokaryotic (eubacterial and archebacterial) genomes in basic features of structure, organization and expression. This is because organellar and nuclear genomes would have shared a common ancestor more recently than organellar and prokaryote genomes. The xenogenous origin hypothesis predicts just the opposite and specifically predicts that organellar genomes should share more synapomorphies with eubacterial than with either nuclear or archebacterial genomes.

Sequence Data

Given the goal of determining whether there are synapomorphes uniting mitochondria or chloroplasts and eubacteria or uniting mitochondria or chloroplasts and nucleus, there are few databases that are found in all three. Basically scientists must look to molecular gene sequences.

But even here, few gene sequence databases fulfill the requirement that the gene in question be encoded in all of the genomes under consideration.

Only the large subunit rRNA (LSU) and the small subunit rRNA (SSU) appear to be ubiquitous (the ribosome is essential for metabolically independent organisms and so is universally distributed from archebacteria to humans). The 5S rRNA genes are absent in mitochondrial genomes other than those of plants and some mtDNAs do not contain a full set of tRNA genes. Moreover, tRNA and 5S RNA are too short to reliably determine phylogeny.

Results of Sequence Analysis

1. The chloroplast appears more closely related to the cyanobacteria than to the rest of the eukaryotic cell, indicating that it is an endosymbiont.

2. Conclusions for the mitochondria are less clearbut they usually appear to be more closely related to aerobic bacteria,

---

The origins of endoplasmic reticulum, golgi, nuclear membranes, chromosomes and mitosis are not known. A few hypotheses have been proposed but, because these are not based on any actual observations, are mere speculation.