Various theories propose that eukaryotes evolved from a prokaryotic ancestor due to a buildup of oxygen in the earth’s atmosphere and/or the build up of toxic waste products during the Proterozoic era. Each theory differs in the mechanism of organelle evolution, but we feel that the serial endosymbiosis theory (SET) is the most plausible. SET proposes mitochondria arose from "purple" bacteria, chloroplasts arose from cyanobacteria, and flagella arose from spirochete bacteria living in symbiosis with an archaebacterium, similar to today’s Thermoplasma bacteria. SET is most plausible due to the abundance of molecular, genetic, and physiological similarities between these protists and eukaryotic organelles.
 

In the Proterozoic Era, 2.5 billion to 544 million years ago, the atmospheric level of oxygen increased to 15% due to oxygen producing cyanobacteria. The levels of oxygen in the atmosphere produced a fatal environment in which anaerobic organisms needed to evolve methods of coping with the presence of oxygen. These organisms evolved to be the organisms know today as eukaryotes. Theories of the evolution of eukaryotic cells include direct filiation, botanical myth, and serial endosymbiosis (SET).

Direct filiation is the classical view of the evolution of eukaryotic organisms. This theory states that all organisms derived directly from a unique ancestral population by the accumulation of single step mutations, and that the same mutational mechanisms known to operate in the evolution of higher animals and plants also operated in the differentiation of higher eukaryotic cells from lower prokaryotic cells (Allsop, 1969; Bold, Alexopoulos, and Delevoryas, 1987; Gore, 1996; Margulis, 1970, 1981). This theory maintains that advantageous mutations, which enabled organisms to survive with oxygen in the atmosphere, were the basis for evolutionary change in prokaryotes.

The second theory, referred to as the "botanical myth" by Lynn Margulis in her 1970 book Early Life (Bessey, 1950; Dougherty and Allen, 1960; Margulis, 1981), states that primitive photosynthetic bacteria evolved gradually into algae and plants, and some of these lost photosynthetic competence and evolved into fungi and animals. Due to the abundance of oxygen in the atmosphere the fungi and animals evolved mitochondria, which utilize oxygen instead of light, as the energy producing organelle.

The third theory of serial endosymbiosis relies on symbiogenesis, or long term symbiotic relationships between different species that lead to new forms of life. This theory, popularized by Lynn Margulis in her 1981 book Symbiosis in Cell Evolution and supported by many authors (Anderson, 1999; Bold et al., 1987; Brockman, 1995; Dyer and Obar, 1994; Gore, 1996; Hacker, 1999; Heidcamp, 1978; Helder, 1999; Kimball, 1999; Luria, 1973; Margulis, 1982, 1970, 1998; Margulis and Sagan, 1995; Melcher, 1999; Mohn, 1999; Penniston, 1997; Wilson, 1974; Zaretsky, 1999), states the following: blue green algae produced oxygen as a by-product of photosynthesis, allowing oxygen to buildup in the atmosphere; other bacteria, prokaryotic cells, developed and grew, some of them with aerobic capabilities; anaerobic, heterotrophic cells known as proto- eukaryotes, ingested these aerobes and developed a mutually beneficial relationship. Ingested organisms that prevented or avoided being digested evolved into the energy producing eukaryotic organelle mitochondria, from proteobacteria, and chloroplasts, from cyanobacteria.

SET also explains the origin of eukaryotic flagella and cilia. Many authors (Brockman, 1995; Kimball, 1999; Margulis, 1982, 1970, 1981, 1998; Margulis and Sagan, 1995; Mohn, 1999; Wilson, 1974; Zaretsky, 1999) propose that flagella derived from the symbiotic relationship of a host cell with a parasitic spirochete. A parasitic spirochete attached to surface of the host cell to gain food through the cell membrane, and the host cell gained motility from its whip-like motions. The beneficial relationship between the organisms evolved in the same manner as that of mitochondria and chloroplasts.

All three theories propose that eukaryotes evolved from a prokaryotic ancestor because of a buildup of toxic substances from waste products such as oxygen and hydrogen ions in the earth’s environment during the Proterozoic era. Each theory differs in the mechanism of organelle evolution, but SET provides the most evidence.

According to the SET developed by Lynn Margulis, the first endosymbiotic merger occurred between a host archaebacterium, similar to Thermoplasma or Sulfolobus prokaryotes, and a swimming bacterium (spirochete). Following this merger, the motile cell entered a symbiosis with an aerobic bacteria, the ancestor of mitochondria, and a symbiosis with a green photosynthetic bacteria, cyanobacteria, the ancestor of chloroplasts (Anderson, 1999; Brockman, 1995; Dyer and Obar, 1994; Gore, 1996; Grun, 1976; Hacker, 1999; Heidcamp, 1978; Kimball, 1999; Luria, 1973; Margulis, 1981, 1982, 1998; Penniston, 1997; Zaretsky, 1999). This combination of bacterial symbionts formed the first algal ancestor.

According to several authors (Anderson, 1999: Brockman, 1995; Dyer and Obar, 1994; Hacker, 1999; Kimball, 1999; Luria, 1973; Margulis, 1981, 1982, 1998; Melcher, 1999; Mohn, 1999; Penniston, 1997) the host cell is believed to be similar to the archaebacteria, Thermoplasma. This theory is supported through shared characteristics of Thermoplasma and eukaryotic cells. Histones in the DNA of Thermoplasma resemble those found in modern eukaryotic cells; introns exist in genes for tRNA, rRNA, and DNA for both types of cells. Also the RNA polymerase in Thermoplasma is similar to the polymerase found in eukaryotes. Further evidence is shown by the actinlike protein in the cytoskeleton, which consists of filaments from six to ten micrometers in diameter, the same as eukaryotic cells.

The evidence supporting the merger of aerobic bacteria, an ancestor of "purple bacteria," and an archaebacteria include mitochondrial replication, genetics, and life cycle as stated by many authors (Anderson, 1999; Brockman, 1995; Birky et.al., 1975; Grun, 1976; Kimball, 1999; Lee et al., 1981; Luria, 1973; Margulis, 1970, 1981, 982, 1998; Margulis and Sagan, 1995; Mohn, 1999; Penniston, 1997; Tzagoloff, 1982; Zaretsky, 1999). Mitochondria replicate independently from the nucleus, arising only from a preexisting mitochondria. They replicate when the environment requires it. Genes encoding for proteins needed by the mitochondria exist in the nucleus of the eukaryotic cell due to gene transfer between the organelle and the nucleus. Evidence for this is found in the production of the ATPase subunit 9 gene. This gene codes for a protein that is required by the mitochondria to produce ATP, however the gene for it is only found in the nucleus of the eukaryotic cell. A mutation occurred in mitochondrial genome ceasing the production of these proteins in the organelle. Mitochondria have different DNA and RNA polymerase than the nucleus of eukaryotic cells. Their ribosomes differ in size from the eukaryotic cell, ranging from 55S to 80S where S is equal to the estimates of molecular size based on density. Mitochondria possess their own circular DNA which ranges from 20,000 to 500,000 base pairs. Circular DNA is unique to prokaryotic cells. This feature and the presence of a double membrane are found in chloroplasts as well as mitochondria.

Multiple authors (Dyer and Obar, 1994; Gore, 1996; Grun, 1976; Hacker, 1999; Kimball, 1999; Margulis, 1981, 1982, 1998; Mohn, 1999) cite evidence for the host cell engulfing the photosynthetic bacteria due to the convenient source of energy, provided by the products of photosynthesis. The organelle has a nucleoid containing multiple copies of circular DNA which range in size from 80 to 275,000 base pairs. This DNA codes for two to four rRNA and 35 tRNA. Unlike mitochondria, however, chloroplasts replicate at the same time as the host cell, however replication of chloroplast DNA and cell DNA are not synchronized. There is a possibility that genetic information has been transferred between the mitochondria and chloroplast. Evidence given by the authors (Raven and Johnson, 1996; Dyer and Obar, 1994; Winckner et.al., 1986) states that the chloroplast followed the mitochondria in endosymbiosis is that chloroplasts are to use the glucose and starch that they produce without the aid of mitochondria.

The most controversial merger in SET occurred between a spirochete and an archaebacterial cell. The theory that spirochete is the ancestor to the flagella is supported by four main authors (Brockman, 1995; Dyer and Obar, 1994; Margulis, 1981, 1982, 1998; Zaretsky, 1999). The theory proposes that a parasitic spirochete attached to the surface of the host bacterium to feed on nutrients within the host, and the host developed locomotion from the whip-like motion of the spirochete. Eventually the spirochete became utterly dependent on the host cell. Supporting evidence for this includes RNA found in the kinetosomes, which give rise to flagella, and DNA found within the cytoplasm of eukaryotes supports the existence of a spirochete symbiosis. Spirochetes contain extremely condensed RNA and give rise to the flagella. Evidence supporting the ancestry of the flagella is the ability of the centriole-kinetosome to repair itself without assistance.

To confirm that organelles were once bacteria look for the following six factors:

1. Enzymes and protein complexes within an organelle are more similar to prokaryotic than to eukaryotic cytoplasm
2. Free living prokaryotes can be found with strong genetic, biochemical and morphological resemblance’s to the organelle
3. Organelles retains a genome more similar to those of a prokaryotic genome.
4. rRNA, tRNA and mRNA within the organelle are similar to those of prokaryotes
5. Organelle has an ability to replicate and genetics that are separate from the host cell
6. Organelle is found in Eukaryotes "all or nothing"- no intermediate stages of the organelle exist.

In 1966, as cited by numerous authors (Mohn, 2000; Dyer and Obar, 1994; Lee et al., 1981), a scientist named Kwang Jeon was raising Amoeba proteus when they became infected with rod shaped bacteria. Infection occurred through phagocytotic ingestion by the amoebae. Bacteria were resistant to lysosomal enzymes and may also have prevented fusion of the vesicles with the lysosomes, allowing for their survival. Most of the amoebae died, but a few survived. These amebas formed a symbiotic relationship with the bacteria by 1971. In forming a endosymbiotic relationship the ameba first reduced the number of bacteria per cell from 150,000 to 42,000.

To test for endosymbiosis, nuclei were extracted from infected amoebae and inserted into normal amoebae. Nuclei could no longer code for or regulate a gene product and amoebae began to die. However, when injected with bacteria, the amoebae revived. At elevated temperatures or in antibodies, the infectious bacteria were killed and the amoebae died. These bacteria have not been able to be cultured free of their hosts. This is strong evidence for the SET.

We believe that SET is the most plausible theory of eukaryotic cell evolution due to the abundance of molecular, genetic, and physiological similarities between the bacteria symbionts and eukaryotic organelles.

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