Up to this point we have touched on only a few of the ways that prokaryotes (bacteria and archaea) differ from eukaryote. The major ones include the fact that eukaryotes have their genetic material isolated from the cytoplasm by a complex double-layered membrane/pore system known as the nuclear envelope (which we will discuss further later on) and the relative locations of chemo-osmotic and photosynthetic systems in the two types of organisms. In prokaryotes, these systems (light absorbing systems, electron transport chains and ATP synthases) are found either within the plasma membrane or within internal membranes derived from the plasma membrane. In contrast, in eukaryotes (plants, animals, fungi, protozoa, and other types of organisms) these structural components are not located on the plasma membrane, but rather within discrete intracellular structures. In the case of the system associated with aerobic respiration, these systems are located in the inner membranes of a double-membrane bound cytoplasmic organelles known as mitochondria. Photosynthetic eukaryotes (algae and plants) have a second type of cytoplasmic organelle (in addition to mitochondria), known as chloroplasts. Like mitochondria, chloroplasts are also characterized by the presence of a double membrane and an electron transport chain located within the inner membrane and membranes apparently derived from it. These are just the type of structures one might expect to see if a bacterial cell was engulfed by the ancestral pro-eukaryotic cell, with the host cell’s membrane surrounding the engulfed cells plasma membrane. A more detailed molecular analysis reveals that the mitochondrial and chloroplast electron transport systems, as well as the ATP synthase proteins, more closely resemble those found in two distinct types of bacteria, rather than in archaea. In fact, detailed analysis of the genes and proteins involved suggest that the electron transport/ATP synthesis systems of eukaryotic mitochondria are homologous to those of ɣ-proteobacteria while the light harvesting/reaction center complexes, electron transport chains and ATP synthesis proteins of photosynthetic eukaryotes (algae and plants) appear to be homologous to those of a second type of bacteria, the photosynthetic cyanobacteria188. In contrast, many of the nuclear systems found in eukaryotes appear more similar to systems found in archaea. How do we make sense of these observations?
Clearly when a eukaryotic cell divides it must have also replicated its mitochondria and chloroplasts, otherwise they would eventually be lost through dilution. In 1883, Andreas Schimper (1856-1901) noticed that chloroplasts divided independently of their host cells. Building on Schimper's observation, Konstantin Merezhkovsky (1855-1921) proposed that chloroplasts were originally independent organisms and that plant cells were chimeras, really two independent organisms living together. In a similar vein, in 1925 Ivan Wallin (1883-1969) proposed that the mitochondria of eukaryotic cells were derived from bacteria. This “endosymbiotic hypothesis” for the origins of eukaryotic mitochondria and chloroplasts fell out of favor, in large part because the molecular methods needed to unambiguously resolve there implications were not available. A breakthrough came with the work of Lynn Margulis (1938-2011) and was further bolstered when it was found that both the mitochondrial and chloroplast protein synthesis machineries were sensitive to drugs that inhibited bacterial but not eukaryotic protein synthesis. In addition, it was discovered that mitochondria and chloroplasts contained circular DNA molecules organized in a manner similar to the DNA molecules found in bacteria (we will consider DNA and its organization soon).
All eukaryotes appear to have mitochondria. Suggestions that some eukaryotes, such as the human anaerobic parasites Giardia intestinalis, Trichomonas vaginalis and Entamoeba histolytica189 do not failed to recognize cytoplasmic organelles, known as mitosomes, as degenerate mitochondria. Based on these and other data it is now likely that all eukaryotes are derived from an ancestor that engulfed an aerobic α-proteobacteria-like bacterium. Instead of being killed and digested, these (or even one) of these bacteria survived within the eukaryotic cell, replicated, and were distributed into the progeny cell when the parent cell divided. This process resulted in the engulfed bacterium becoming an endosymbiont, which over time became mitochondria. At the same time the engulfing cell became dependent upon the presence of the endosymbiont, initially to detoxify molecular oxygen, and then to utilize molecular oxygen as an electron acceptor so as to maximize the energy that could be derived from the break down of complex molecules. All eukaryotes (including us) are descended from this mitochondria-containing eukaryotic ancestor, which appeared around 2 billion years ago. The second endosymbiotic event in eukaryotic evolution occured when a cyanobacteria-like bacterium formed an relationship with a mitochondria-containing eukaryote. This lineage gave rise to the glaucophytes, the red and the green algae. The green algae, in turn, gave rise to the plants.
As we look through modern organisms there are a number of examples of similar events, that is, one organism becoming inextricably linked to another through endosymbiotic processes. There are also examples of close couplings between organisms that are more akin to parasitism rather then a mutually beneficial interaction (symbiosis)190. For example, a number of insects have intracellular bacterial parasites and some pathogens and parasites live inside human cells191. In some cases, even these parasites can have parasites. Consider the mealybug Planococcus citri, a multicellular eukaryote; this organism contains cells known as bacteriocytes. Within these cells are Tremblaya princeps type β-proteobacteria. Surprisingly, within these Tremblaya bacterial cells, which lie within the mealybug cells, live Moranella endobia-type γ-proteobacteria192. In another example, after the initial endosymbiotic event that formed the proto-algal cell, the ancestor of red and green algae and the plants, there have been endocytic events in which a eukaryotic cell has engulfed and formed an endosymbiotic relationship with eukaryotic green algal cells, to form a “secondary” endosymbiont. Similarly, secondary endosymbionts have been engulfed by yet another eukaryote, to form a tertiary endosymbiont193. The conclusion is that there are combinations of cells that can survive better in a particular ecological niche than either could alone. In these phenomena we see the power of evolutionary processes to populate extremely obscure ecological niches in rather surprising ways.