Prokaryote cells were the first life form to appear on Earth, 3500x106 years ago. Prokaryote means before the nucleus, which means that they do not have DNA enclosed by an inner membrane. The organization of prokaryotic cells is quite simple: a plasma membrane confines an inner space where chemical reactions take place. They also have a capsule lining the extracellular surface of the plasma membrane. Furthermore, protein structures such as flagella and pili, for cell movement and DNA exchange, respectively, can sometimes be observed. Prokaryotes were the only cell type at the beginning of life on Earth. Two main groups of prokaryotes are known: bacteria and archaea.
Eukaryotic cells appeared 1500-2000x106 years ago. It is about 1500x106 later than prokaryotes. The cell organization of eukaryotes was something new on Earth, showing so many innovations that they opened new evolutionary ways not explored by living forms so far. In evolution, these breakthroughs are known as evolutionary transitions. Eukaryotic cells reached a complex morphological organization, including internal membrane-bound compartments, nucleus as a key component, and built a sophisticated cytoskeleton. They were also able to incorporate a huge amount of external DNA, whole genomes that gave rise to mitochondria and chloroplasts, discovered sexual reproduction, and, by grouping together, gave rise to a new type of life form: pluricellular organisms, which independently appeared several times during evolution.
2. From who?
How eukaryotes arose is not known, but it should have happened as a result of the collaboration between the two cell types present at that time: archaea and bacteria. Eukaryotes are monophyletic, which means that all of them, including plants, animals, fungi, algae, and unicellular eukaryotes, descended from a common ancestor known as LECA (Last Eukaryotic Common Ancestor). So, with the evidences we have today, the eukaryote cell was "invented" only once during evolution. Comparison of cell genomes of today's phylogenetically distant eukaryotes suggests that LECA had a genome as complex and rich as the genome of the current cells, and probably it had similar morphology and structure.
There is no doubt that LECA evolved from prokaryotes, but from which one, bacteria or archaea? Choosing one of them is not easy (Figure 1). Current eukaryotes are like chimeras because genes from both types of prokaryotes coexist in the same eukaryotic nucleus. For example, genes involved in processing eukaryotic DNA, such as replication, transcription and translation (known as informational genes) are more similar to those of archaea, while those genes in charge of the eukaryotic metabolism, such as energy and synthesis of amino acids, lipids and nucleotides (known as operational genes), are more similar to the genes of bacteria. To get things more complicated, even the archaea-like genes may have come from different groups of archaea.
Phylogenetic studies (comparison of DNA sequences) suggest that eukaryotes emerged from a group of archaea named the Asgard group, which has recently been discovered. This group includes the lokiarchaea. They have been found to be the prokaryotes most closely related to eukaryotes when comparing informational genes such as those involved in metabolism and DNA processing. Furthermore, some authors suggest that these genes are primarily transmitted through generations of descendants rather than horizontally (between non-related cells). That is why these genes are good tools for determining more accurate evolutionary relationships between organisms. Lokiarchaeota also has genes homologous to those eukaryote genes related to cytoskeleton and membrane remodeling. Curiously enough, although a lokiarchaea cell has not yet been seen, it has been guessed by metagenomic analysis. To do this, water close to hydrothermal vents was collected and the DNA it contained was studied: it was sequenced and assembled. So, we have the DNA, but not yet the cell. These environments are poor in oxygen, suggesting that the eukaryote ancestor lived in anoxic waters. Only after they got oxygenic bacteria as endosymbionts (the future mitochondria) were they able to populate more oxygenated places. Since lokiarchaeas have not been observed, their structural complexity or even cell size cannot be compared with those of eukaryotes.
However, in the eukaryotic nucleus, there are 2 to 3 times more genes from bacteria than from archaea. Furthermore, eukaryotic membranes do not contain isoprenoid chains in their fatty acids or ether linkages in membrane lipids, both of which are typically found in archaea membranes. In fact, it can be said that eukaryotes have membranes more similar to those of bacteria. Authors supporting the archaea-bacteria fusion theory suggest that while genes for DNA processing come from archaea, genes for metabolism, including membrane synthesis, come from bacteria. It means that there is not a development of an archaea group to give a proto-eukaryote, but a completely new type of cell that emerged after the fusion of two distant lineages
There is a key event during the emergence of LECA: how was the impact of the endosymbiosis of the mitochondrial ancestor? Some authors claim that this event was essential for the cells to become LECA, whereas others propose that the cell engulfing the mitochondrial ancestor already had a complex genome and well-developed cell structure. Therefore, the first endosymbiosis was just ono more step towards becoming LECA (Figure 2). There are many theories about how the evolutionary process that gave rise to LECA happened. They can be summarized in two:
Symbiosis model (or 2D model). This model proposes the direct fusion of an archaea and a bacterium, which means that there is no protoeukaryote. In this scenario, two distant branches of the tree of life merged, leading to the emergence of a completely new branch of cells. There is some evidence supporting this proposal. Nowadays, the presence of bacteria containing other prokaryotes as endosymbionts has been described. The fusion event boosted the increase in cellular complexity, the bacterium became the mitochondria. Both cells shared different cellular activities: archaea were in charge of DNA and bacteria dealt with metabolism. There is another version of this model in which there was no initial endosymbiosis event, but rather a long period of time in which these two cells cooperated together. During this time, horizontal gene transfer (exchange of genes) was possible because they were spatially close. In this version of the model, the hydrogen hypothesis is suggested. The bacterium produced hydrogen for the archaea metabolism, and the archaea produced organic molecules for the bacterium. Eventually, the bacterium was included into the archaea, which already had many bacterial genes. It is not yet clear how this endosymbiosis took place. Phagocytosis has been assumed as the process of endosymbiosis, but there is no experimental evidence for this.
Autogenous model (3D model). Protoeukaryotic cells arose from a common ancestor with archaea by a progressive increase in complexity, so that they somehow became similar to modern eukaryotes. These cells had an endomembrane system, a nucleus, and a cytoskeleton, but they did not have mitochondria. They were able to feed by phagocytosis. In one occasion, they engulfed an alfa-proteobacterium that was not digested and became an endosymbiont, thus representing the ancestor of current mitochondria. Over time, many genes from the endosymbiont were transferred to the nucleus and they took the control of cellular metabolism, but not DNA managing. However, intermediate forms between eukaryotes and prokaryotes have yet been found, and, even more relevant, eukaryotic cells without mitochondria have not been discovered (there are some eukaryotic cells without mitochondria, but they have other organelles derived from mitochondria).
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