7.5: Eukaryotic Origins

Eukaryotic Origins

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Learning Objectives

• List the unifying characteristics of eukaryotes
• Describe what scientists know about the origins of eukaryotes based on the last common ancestor
• Explain endosymbiotic theory

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, the comparative biology of extant organisms and the limited fossil record provide some insight into the history of Eukarya.

The earliest fossils of living organisms 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.

These characteristics that are common to nearly all eukaryotes include:

1. Cells with nuclei that are 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 currently living eukaryotes have cells with nuclei.
2. Mitochondria. An organelle that processes glucose using oxygen to produce ATP. 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 there is molecular evidence that 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 based on information contained in their DNA.
6. Mitosis, which is a process of cellular division wherein replicated chromosomes are divided and separated into two new cells using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sexual reproduction and meiosis, a process of cell division and genetic recombination unique to eukaryotes.

Endosymbiosis and the Evolution of Eukaryotes

To understand eukaryotic organisms, it is necessary to understand that all extant (currently living) eukaryotes are descendants of an 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 if the two organisms 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 such as plants. Before explaining this further, it is necessary to consider metabolism in prokaryotes.

Prokaryotic Metabolism

Prokaryotes are much more metabolically diverse than eukaryotes. This makes sense when considering that the evolution of eukaryotes represents only one branch of the tree of life, and a relatively recent one at that.

Many important metabolic processes such as nitrogen fixation, are never found in eukaryotes. One that is not unique to eukaryotes (i.e., some prokaryotes can do it), but that is present in all eukaryotes is the process of aerobic respiration and it happens in the mitochondria. This suggests that the ability to respire came from a type of prokaryote that could do aerobic respiration; they eventually became the eukaryotic cell’s mitochondria. This is discussed in more detail below. 

The Problem with Oxygen

While today’s atmosphere is about one-fifth molecular oxygen (O₂), geological evidence shows that the atmosphere originally lacked O₂. Without oxygen, aerobic respiration would not be possible, and prokaryotes would have relied on fermentation as a means of transforming the energy in their food into something that they use for their cells. At some point around 3.5 billion years ago, some prokaryotes began using energy from sunlight to power the formation of organic compounds. That is, they evolved the ability to photosynthesize. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O₂ as a waste product. They used chemical gradients across their cell membrane to do it.

Eventually, the amount of photosynthetic oxygen built up in some environments to levels that were toxic to the organisms living at that time. Oxygen is reactive (it is a strong electron acceptor) and can damage many organic compounds. Metabolic processes evolved to protect organisms from oxygen. Aerobic respiration, one of these processes, utilized the newly available chemical, and its properties as an electron acceptor, to extract energy out of reduced chemicals (a reduced chemical is one that contains many electrons). As energy was extracted from these reduced chemicals, the cell captured the energy to make ATP, a chemical it could readily use to power its processes. This ability to use oxygen to process reduced chemicals (i.e., aerobic respiration) became widely present among prokaryotes, including in a group we now call alpha-proteobacteria (described below).

Organisms that did not evolve aerobic respiration  continued to exist, but the were restricted to living in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active. By about 2 billion years ago, however, geological evidence shows that oxygen built up to higher concentrations in the atmosphere. This is known as the Great Oxygenation Event (GOE) (Figure \(\PageIndex{1}\)). Even though levels were rising, oxygen amounts similar to today’s only arose within the last 600 Ma just before the beginning of the Cambrian Period.

Recall that the first fossils that we believe to be eukaryotes date to about 2 Ga, so they appeared during the GOE. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by scientists in the late 1800s, where they were described as somewhat worm-shaped structures that moved around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.

Figure \(\PageIndex{1}\): The oxygen concentration in Earth’s atmosphere rose sharply around 300 million years ago. The red dotted line indicates current levels of oxygen in the atmosphere for reference.

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, biologist Lynn Margulis proposed the endosymbiotic theory, suggesting that eukaryotes were the product of one cell engulfing another. In the proposed model, once engulfed, the two cells continued to live together and evolved co-dependence so that they could no longer live independently of one another. Although Margulis’ work initially was met with resistance, this once-revolutionary hypothesis is now widely accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. 

Broadly, it has become clear that many of the nuclear genes and the molecular machinery responsible for replication and the expression of those genes 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 all eukaryotes.

Video

This 8-minute video provides an overview of the steps in the evolution of eukaryotes from prokaryotes.
Question after watching: Which organelle do you think evolved first: chloroplasts that photosynthesize or mitochondria that extract energy from reduced chemicals using oxygen? What is your rationale?

Evidence for Endosymbiosis: 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 (µm) in length and exists in the cell as an organelle that can be ovoid, worm-shaped, or intricately branched (Figure \(\PageIndex{2}\)).

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.

Alpha-proteobacteria are a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Most mitochondria are shaped like alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.

Figure \(\PageIndex{2}\): 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 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 like 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.

Some living eukaryotes are anaerobic and cannot survive in the presence of oxygen. Some appear to lack organelles that could be recognized as mitochondria. In the 1970s to the early 1990s, many biologists suggested that some of these eukaryotes were descended from ancestors whose lineages had diverged from the lineage of mitochondrion-containing eukaryotes before endosymbiosis occurred. However, later findings suggest that reduced organelles are found in most, if not all, anaerobic eukaryotes, and that all eukaryotes appear to carry some genes in their nuclei that are of mitochondrial origin. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes. Therefore, most biologists now accept that the last common ancestor of eukaryotes had mitochondria.

Evidence of Endosymbiosis: 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 \(\PageIndex{3}\)).

 

Figure \(\PageIndex{3}\): (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. This likely happened twice in the history of eukaryotes. 

Cyanobacteria are a group of Gram-negative 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 (Figure \(\PageIndex{4}\)). Cyanobacteria also have the peptidoglycan wall and lipopolysaccharide layer associated with Gram-negative bacteria.

Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes like those of cyanobacteria. Each chloroplast is surrounded by two membranes. 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 the engulfing of the chloroplast ancestor occurred 1 to 1.5 billion years ago, at least 500 million years after the fossil record suggests that eukaryotes were present.

Figure \(\PageIndex{4}\): (a) Red algae and (b) green algae (visualized by light microscopy) share similar DNA sequences with photosynthetic cyanobacteria. Scientists speculate that, in a process called endosymbiosis, an ancestral prokaryote engulfed a photosynthetic cyanobacterium that evolved into modern-day chloroplasts. (credit a: modification of work by Ed Bierman; credit b: modification of work by G. Fahnenstiel, NOAA; scale-bar data from Matt Russell)

Optional Activity

Figure \(\PageIndex{5}\): 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?

Answer

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

Video

This 4.5-minute video provides a quick overview of the differences between prokaryotes and eukaryotes.
Question after watching: What do the characteristics contained in both prokaryotes and eukaryotes tell you about the evolution of life on earth?