It is believed that all organisms have evolved from a cell type that appeared about 3500x106 years ago, known as LUCA (Last Universal Common Ancestor). This cell must have been simple and supposedly similar to current prokaryotes. However, the complexity of some of these early cells increased with time, leading to the appearance of eukaryotic cells. All current eukaryotic cells are believed to originate from one of these early cells, which is called LECA (Last Eukaryotic Common Ancestor).
Current eukaryotic cells have internal membrane-bound compartments such as the nucleus, and various organelles such us endoplasmic reticulum, Golgi apparatus, endosomes, mitochondria, chloroplasts, as well as cytoskeleton. The oldest fossils of eukaryotic cells found suggest that they were already present about 1500x106 years ago, but it is plausible that eukaryotic cells appeared much earlier.
It is widely accepted that some organelles of eukaryotic cells emerged by endosymbiosis. Mereschokovsky (1905, 1910) was the first to propose that chloroplasts are the descendants of a prokaryotic cell incorporated by a eukaryotic cell. He named this process as symbiogenesis, which later led to the term endosymbiosis. Thus, both mitochondria and chloroplasts are derived from free ancient prokaryotic cells that were incorporated by other cells and evolved into intracellular organelles. Some authors have postulated that peroxisomes, cilia and flagela were also originated by symbiosis processes, although there is little experimental support.
The endosymbiosis theory is supported by some similarities between current bacteria with mitochondria and chloroplasts. For example, both organelles have similar sizes than bacteria, circular strands of DNA inside, and 70S ribosomes. Furthermore, both organelles are able of dividing independently inside the eukaryotic cytoplasm. The double membrane of mitochondria and chloroplasts does not mean that one is from the ancient bacterium and the other from the host. Actually, in the case of chloroplasts, both membranes are thought to belong to the ancient bacterium, which only lost the peptidoglycan. These two organelles evolved from ancient free bacteria that were incorporated or entered into other larger cells (mitochondrium into an archaea and chloroplast into a eukaryotic cell). The two cellular types became so dependent between each other that they only could live together. Mitochondria ancestors could be the ancestors of the current alfa-proteobacteria and the ancestors of chloroplasts could be the ancestors of the current cyanobacteria.
The endosymbiosis theory postulates an initial fusion of two prokaryotic cells, most probably between a bacterium and an archaea (Figure 1). It likely happened after a long period of metabolic collaboration between both types of cells, so that there was a symbiosis (no endosymbiosis yet) before the fusion. After the fusion, the cell developed a complex system of membranous organelles and a cytoskeleton, and the bacterium became the current mitochondria. Thus, we would have an eukaryotic cell. Subsequently, there was a second colonization in some of these eukaryiotic cells by prokaryotes containing chlorophyll, probably similar to the current cyanobacteria, which over the time become transformed into the current chloroplasts. These cells with two endosymbiosis processes are the photosynthetic cells of plants, algae and unicellular photosynthetic cells.That is, there have been two successive endosymbiosis, which is why some authors regard plant cells as well-organized microbial communities.
Today, even more complex cellular communities are known. A primary endosymbiosis (not to be confused with the first endosymbiosis) results from the association of two free cells, one of them ends up inside the other (Figure 2). Over the time, part of the DNA is transferred between the two cells and evolves to maintain the endosymbiosis. Three primary endosymbiosis are known. Mitochondria and chloroplasts are the result of the two most widspread primary endosymbiosis. They also had a deep impact in the cell lineages evolution. There is a third primary endosymbiosis of an alpha-cynabacterium and the eukaryote Paulinella chromatophora. In the three cases, the incorporated cells transferred or lost genes, but kept those essential, for example, for division and DNA processing. A secondary endosymbiosis (not to be confused with the second endosymbiosis) happened when an eukaryotic cell with mitochondria and chloroplasts engulfed another eukaryotic cell that also contained mitochondria and chloroplasts (Figure 2). The engulfed cell became endosymbiont, lost its nucleus or was atrophied, and its chloroplasts started to work for and depend on the host cell. Currently, three independent events of secondary endosymbiosis are known. Tertiary endosymbiosis happened when a eukaryotic cell incorporated another eukaryotic that was the result of a previous secondary endosymbiosis. There are living examples in nature of all these types of endosymbiosis.
It should be noted, however, that current mitochondria and chloroplasts are quite different from current aerobic bacteria and cyanobacteria, respectively. For example, current cyanobacteria contain about 3000 genes, whereas chloroplasts only have about 100 - 200 genes. The genes that remain in the chloroplast only code for about 10 % of its proteins. This is because many genes were trasnferred from the chloroplast to the host cell nucleus, which now synthesizes many proteins needed by the chloroplast. It is a very complex mechanism since the transferred genes have to be expressed in a completely different environment and their products have to travel the cytosol, enter the chloroplast, and carry out their functions in different compartments inside the endosymbiont. However, it is advantageous for the host cell because it takes the control over the functions and proliferation of chloroplasts. A similar phenomenon has ocurred with the mitochondria.
Nowadays, there are many examples of bacteria, but none of archaea, living inside eukaryote cells as endosymbionts, even bacteria inside archaea. However, none of them have reached the degree integration of mitochondria and chloroplasts. All of them are different ways of cooperation between different types of cells explored by evolution. Whatever the relationship, the endosymbiont provides molecules that the host needs. For example, many invertebrates have bacteria that are intracellular, which can complete their life cycle and can even be transmitted to the offspring included in gametes. They are so well adapted that are harmless to the host, being sometimes beneficial or even essential. Actually, it is like an infection without significant collateral damages to the hosts, although they use the same molecular machinary as pathogenic bacteria for their proliferation. There are some examples of endosymbiosis involving two eukaryotes as well. For example, a paramecium (Bursaria) houses algae (Chlorella). Propelled by cilia, the paramecium always moves to illuminated places where algae take advantage of the high intensity of light to carry out photosynthesis and the paramecium take advantage of the resulting products. There are many other examples. Some symbionts are called secondary and are not permanent. They produce horizontally invasions, that is, they can jump to a different host. In this case, their DNA is not as large as of free bacteria, nor as small as that of other more integrated endosymbionts.
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