Biologists have long been aware of the vast gulf between cells with a nucleus and other organelles, and the much tinier cells which lack both those features. Indeed, many biologists have expressed sentiments like the following: “The greatest evolutionary discontinuity [i. e. gap] between living organisms is that separating prokaryotic and eukaryotic cells.”
Naturally this situation has attracted a lot of attention and there has been much theorizing. In 1967 Lynn Margulis published a proposal that the mitochondrion in all eukaryotic cells, and the plastid (chloroplast) in plant cells were actually formerly independent organisms which had been engulfed by a different kind of cell. The engulfed victims however did not die but managed to survive and actually contribute to the health of the host cell. Thus, was born the endosymbiosis theory to account for the origin of the eukaryotic cell. There are many serious problems with this theory but this has not discouraged enthusiastic support for the idea.
The starting point for such a scenario is two tiny prokaryotic cells. They each have a rigid wall to protect the cell inside. Neither engulfs anything, nor is it big enough to do such a thing. Some assumptions are thus needed to explain the engulfing event. Firstly, one of the cells would need to discard its rigid cell wall and to grow larger and to develop a flexible plasma membrane which would enable it to engulf a small cell. These are major changes that would require a lot of new skills in the engulfing cell. The victim cell however was not digested. It stayed around, lost its cell wall, and degenerated into possibly a mitochondrion or possibly a chloroplast (if the engulfed cell was photosynthetic). There is one piece of information which encouraged people to support this scenario. Mitochondria and chloroplasts today contain some DNA, in a ring like prokaryotes, and they contain some ribosomes, protein manufacturing machines that resemble prokaryote ribosomes. What more was there to say? Plenty.
A major problem is that most of the genes controlling the activities of the mitochondrion and chloroplast are in the host nucleus, not in the organelles that supposedly came from the engulfed cell. The endosymbiosis theory accounts for this problem by insisting that the engulfed cell lost most of its genes to the host nucleus. Those genes were somehow incorporated into the genetic material in the host nucleus and subsequently lost from the original engulfed cell. One eminent scientist reflected on this situation: “But the migration of genes from endosymbionts to the nucleus is remarkable because it seems to have raised more difficulties than it solved. Once the transfer occurred, the proteins encoded by these genes began to be manufactured in the cytoplasm of the host cell (where the products of all nuclear genes are constructed.) These molecules had then to migrate into the endosymbionts to be of use.” [Christian de Duve. 1996. The Birth of Complex Cells. Scientific American April pp. 50-57. See p. 57] But, importing large organic molecules through the membrane surrounding mitochondria or chloroplasts is not a simple task. The molecule that needs to move through the membrane must be equipped with a targeting signal tail that receptors in the membrane recognize in order to allow passage. (This is yet more information that must somehow be instantly created to allow the system to work.]
There are still some specialists in the field who doubt that the mitochondrion came about through an endosymbiotic event. However, these same people are convinced that the chloroplast in plant cells did develop through such a process. Nevertheless, they consider that the engulfing cell by this time was already a eukaryote. “Unlike the origin of mitochondria, the details of which are still debated, there is no longer any doubt that plastids are derived from once free-living cyanobacteria and that the host cell was a full-blown eukaryote with a nucleus, cytoskeleton and mitochondrion.” [John M. Archibald. 2009. The Puzzle of Plastid Evolution. Current Biology 19: R81-R89 See p. R81.] The reason that these people are so certain about endosymbiosis of the chloroplast is that the origin of photosynthesis is so hard to explain even once, that even unlikely endosymbiosis events (serial endosymbiosis) are preferable to explaining multiple origins of photosynthesis. [The collection of light catching pigments in many diverse algae are so different that serial endosymbiotic events are used to explain the origin of these elaborate systems. Green algae and land plants make use of the same set of pigments, but red algae, brown algae, yellow-green algae, golden algae and others all exhibit different sets of pigments. Cyanobacteria share chlorophyll a with the algae and land plants, but there are various other photosynthetic bacteria that use all different pigments.]
Once molecular biologists discovered that there is some DNA inside chloroplasts, this was assumed to be proof that endosymbiosis had occurred. It soon became apparent, however, that most genes controlling the activities of the chloroplast, in fact come from the host nucleus. This was the beginning of a realization of the scope of the problem where the majority of proteins needed by an organelle have to be transported from the cytoplasm into that organelle. Thus “The plastid is a crucial organelle in plant cells ….. However most plastid proteins (over 90%) are encoded by the nuclear genome and are imported into plastids from the cytosol postranslationally.” [Dong Wook Lee et al. 2009. Plant Physiology 151 #1 p. 129]
The story for the evolution of plastids and chloroplasts starts with a primary endosymbiotic event in which a hungry eukaryote engulfs a cyanobacterium. Most of the genes from the cyanobacterium then transfer to the host nucleus, leaving a small number of genes on the DNA in the cyanobacterium (now plastid). For some other algae with different photosynthetic pigments, there follows a secondary endosymbiosis event involving a eukaryote with green photosynthetic genes which engulfs a cell with a red chloroplast. The genes that are in the chloroplast of the newly engulfed cell once again move to the secondary or tertiary host nucleus and the genes from the original cyanobacterium completely disappear from the chloroplast.
We can see the problem with this scenario from the following assertion: “One of the most intriguing aspects of secondary and tertiary endosymbiosis is the fate of the endosymbiont [hostage] nucleus and the essential genes it harbors. Most secondary- and tertiary-plastid-containing organisms have completely done away with the primary algal nucleus that accompanied the plastid. Consequently, the hundreds of plastid genes that moved from the original cyanobacterial endosymbiont to the host nucleus during primary endosymbiosis must have moved again, this time from the primary host nucleus to that of the secondary host.” [Archibald. 2009. R83]
It is apparent from the insurmountable problems with the endosymbiosis theory that it would have been rejected long ago if it were not for the need of biologists to come up with an evolutionary scenario to explain the extremely complex eukaryotic cell inclusions. Developing photosynthesis even once was a major miracle. Scientists would not want to be stuck proposing several such origins for organisms with differently coloured light catching pigments.