Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into the history of Eukarya.

The earliest fossils found appear to be Bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10 µm or greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.

Characteristics of Eukaryotes

Data from these fossils have led comparative biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at least some of the members of each major lineage.

1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
3. A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but they are descended from ancestors that possessed them.
5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus.
8. Some have cell walls. It might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enough is known about eukaryotes’ cell walls and their development to know how much homology exists among them. Homology is the existence of shared ancestry between a pair of structures in different organisms (a similarity that stems from evolution). If the last common ancestor could make cell walls, it is clear that this ability must have been lost in many groups (most obviously animal cells).

Endosymbiosis and the Evolution of Eukaryotes

In order to understand eukaryotic organisms fully, it is necessary to understand that all living eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes.

Endosymbiotic Theory

As cell biology developed in the twentieth century, it became clear that mitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotic theory, which states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initially was met with resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much still remains to be discovered about the origins of the cells that now make up the cells in all living eukaryotes.

Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those in Archaea. On the other hand, the metabolic organelles and genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, it is not known whether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.

Mitochondria

One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometers in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched (Figure 1).

Figure 1. In this transmission electron micrograph of mitochondria in a mammalian lung cell, the cristae, infoldings of the mitochondrial inner membrane, can be seen in cross-section. (credit: Louise Howard)

Mitochondria arise from the division of existing mitochondria; they may fuse together; and they may be moved around inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic prokaryote, specifically an alpha-proteobacterium, thereby giving the host cell the ability to use oxygen to release energy stored in nutrients.

Mitochondria divide independently by a process that resembles binary fission in prokaryotes. Specifically, mitochondria are not formed from scratch (de novo) by the eukaryotic cell; they reproduce within it and are distributed with the cytoplasm when a cell divides or two cells fuse. Therefore, although these organelles are highly integrated into the eukaryotic cell, they still reproduce as if they are independent organisms within the cell. However, their reproduction is synchronized with the activity and division of the cell. Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living prokaryotes.

Mitochondria that carry out aerobic respiration have their own genomes, with genes similar to those in alpha-proteobacteria. However, many of the genes for respiratory proteins are located in the nucleus. When these genes are compared to those of other organisms, they appear to be of alpha-proteobacterial origin. Additionally, in some eukaryotic groups, such genes are found in the mitochondria, whereas in other groups, they are found in the nucleus. This has been interpreted as evidence that genes have been transferred from the endosymbiont chromosome to the host genome. This loss of genes by the endosymbiont is probably one explanation why mitochondria cannot live without a host.

Plastids

Some groups of eukaryotes are photosynthetic. Their cells contain, in addition to the standard eukaryotic organelles, another kind of organelle called a plastid. When such cells are carrying out photosynthesis, their plastids are rich in the pigment chlorophyll a and a range of other pigments, called accessory pigments, which are involved in harvesting energy from light. Photosynthetic plastids are called chloroplasts (Figure 2).

Figure 2. (a) This chloroplast cross-section illustrates its elaborate inner membrane organization. Stacks of thylakoid membranes compartmentalize photosynthetic enzymes and provide scaffolding for chloroplast DNA. (b) In this micrograph of Elodea sp., the chloroplasts can be seen as small green spheres. (credit b: modification of work by Brandon Zierer; scale-bar data from Matt Russell)

Like mitochondria, plastids appear to have an endosymbiotic origin. This hypothesis was also championed by Lynn Margulis. Plastids are derived from cyanobacteria that lived inside the cells of an ancestral, aerobic, heterotrophic eukaryote. This is called primary endosymbiosis, and plastids of primary origin are surrounded by two membranes. The best evidence is that this has happened twice in the history of eukaryotes. In one case, the common ancestor of the major lineage/supergroup Archaeplastida took on a cyanobacterial endosymbiont; in the other, the ancestor of the small amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial endosymbiont. Almost all photosynthetic eukaryotes are descended from the first event, and only a couple of species are derived from the other.

Cyanobacteria are a group of bacteria with all the conventional structures of the group. However, unlike most prokaryotes, they have extensive, internal membrane-bound sacs called thylakoids. Chlorophyll is a component of these membranes, as are many of the proteins of the light reactions of photosynthesis. Cyanobacteria also have the peptidoglycan wall and lipopolysaccharide layer associated with bacteria.

Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes similar to those of cyanobacteria. Each chloroplast is surrounded by two membranes. In the group of Archaeplastida called the glaucophytes and in Paulinella, a thin peptidoglycan layer is present between the outer and inner plastid membranes. All other plastids lack this relictual cyanobacterial wall. The outer membrane surrounding the plastid is thought to be derived from the vacuole in the host, and the inner membrane is thought to be derived from the plasma membrane of the symbiont.

There is also, as with the case of mitochondria, strong evidence that many of the genes of the endosymbiont were transferred to the nucleus. Plastids, like mitochondria, cannot live independently outside the host. In addition, like mitochondria, plastids are derived from the division of other plastids and never built from scratch. Researchers have suggested that the endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion years ago, at least 5 hundred million years after the fossil record suggests that eukaryotes were present.

Practice Question

Figure 3. The first eukaryote may have originated from an ancestral prokaryote that had undergone membrane proliferation, compartmentalization of cellular function (into a nucleus, lysosomes, and an endoplasmic reticulum), and the establishment of endosymbiotic relationships with an aerobic prokaryote, and, in some cases, a photosynthetic prokaryote, to form mitochondria and chloroplasts, respectively.

What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?

Show Answer

All eukaryotic cells have mitochondria, but not all eukaryotic cells have chloroplasts.

Secondary Endosymbiosis in Chlorarachniophytes

Endosymbiosis involves one cell engulfing another to produce, over time, a coevolved relationship in which neither cell could survive alone. The chloroplasts of red and green algae, for instance, are derived from the engulfment of a photosynthetic cyanobacterium by an early prokaryote.

This leads to the question of the possibility of a cell containing an endosymbiont to itself become engulfed, resulting in a secondary endosymbiosis. Molecular and morphological evidence suggest that the chlorarachniophyte protists are derived from a secondary endosymbiotic event. Chlorarachniophytes are rare algae indigenous to tropical seas and sand that can be classified into the rhizarian supergroup. Chlorarachniophytes extend thin cytoplasmic strands, interconnecting themselves with other chlorarachniophytes, in a cytoplasmic network. These protists are thought to have originated when a eukaryote engulfed a green alga, the latter of which had already established an endosymbiotic relationship with a photosynthetic cyanobacterium (Figure 4).

Figure 4. The hypothesized process of endosymbiotic events leading to the evolution of chlorarachniophytes is shown. In a primary endosymbiotic event, a heterotrophic eukaryote consumed a cyanobacterium. In a secondary endosymbiotic event, the cell resulting from primary endosymbiosis was consumed by a second cell. The resulting organelle became a plastid in modern chlorarachniophytes.

Several lines of evidence support that chlorarachniophytes evolved from secondary endosymbiosis. The chloroplasts contained within the green algal endosymbionts still are capable of photosynthesis, making chlorarachniophytes photosynthetic. The green algal endosymbiont also exhibits a stunted vestigial nucleus. In fact, it appears that chlorarachniophytes are the products of an evolutionarily recent secondary endosymbiotic event.

The plastids of chlorarachniophytes are surrounded by four membranes: The first two correspond to the inner and outer membranes of the photosynthetic cyanobacterium, the third corresponds to the green alga, and the fourth corresponds to the vacuole that surrounded the green alga when it was engulfed by the chlorarachniophyte ancestor. In other lineages that involved secondary endosymbiosis, only three membranes can be identified around plastids. This is currently rectified as a sequential loss of a membrane during the course of evolution.

The process of secondary endosymbiosis is not unique to chlorarachniophytes. In fact, secondary endosymbiosis of green algae also led to euglenid protists, whereas secondary endosymbiosis of red algae led to the evolution of dinoflagellates, apicomplexans, and stramenopiles.