Table of Contents
Historical background and basic idea
The endosymbiotic theory explains how complex eukaryotic cells (with nucleus, mitochondria, and often chloroplasts) arose from simpler prokaryotic ancestors. Within symbiogenesis, it is a specific hypothesis: key eukaryotic cell structures originated when once‑free‑living prokaryotes entered into long‑term, internal symbioses and gradually became permanent cell organelles.
Important aspects of the basic idea:
- A large, host prokaryote took up smaller bacteria by phagocytosis or a similar engulfment process.
- Instead of being digested, some of these bacteria survived inside the host cell.
- This started a mutualistic relationship: both partners gained advantages.
- Over long evolutionary time, the internal bacteria lost their independence, transferred many genes to the host’s chromosomes, and became organelles (mitochondria, plastids such as chloroplasts).
The theory mainly addresses three major evolutionary innovations:
- Origin of mitochondria
- Origin of chloroplasts and other plastids
- Possible endosymbiotic origin of other structures (especially the double‑membrane “nucleus‑like” organization and some flagella‑related components, though these are more debated).
Stepwise scenario: from prokaryotes to the first eukaryotes
1. The host cell: an archaeal ancestor
Comparisons of DNA and ribosomal RNA sequences indicate that the host that first acquired mitochondria was most closely related to Archaea. Today, a group called Asgard archaea (e.g., Lokiarchaeota) is considered particularly relevant because:
- Their genomes encode many proteins previously thought to be unique to eukaryotes (involved in membrane remodeling, cytoskeleton, and trafficking).
- This suggests that the ancestral archaeal host already had some ability to form complex internal membrane structures and to engulf other cells.
Thus, the first step toward eukaryotes seems to have been:
- An archaeal lineage evolved increased cellular complexity and a more flexible cell surface.
- This flexibility enabled closer interactions (possibly engulfment) with bacteria.
2. Acquisition of mitochondria
The best‑supported endosymbiotic event is the origin of mitochondria.
Key points of the mitochondrial origin:
- The endosymbiont was a bacterium from within the Alphaproteobacteria.
- The host was an archaeal cell that already had some complexity.
- The engulfed bacterium initially functioned as an internal partner specializing in energy metabolism, especially aerobic respiration.
Mutual benefits:
- For the host:
- Access to highly efficient ATP production via oxidative phosphorylation.
- Ability to exploit oxygen as a powerful electron acceptor, giving an advantage in oxygen‑rich environments.
- For the bacterium:
- A stable environment with access to substrates from the host’s metabolism.
- Physical protection from outside stresses.
Over time:
- Many bacterial genes were either lost or transferred to the host’s genome (nuclear genome now encodes most mitochondrial proteins).
- Mitochondria became obligatory parts of the cell; they can no longer live independently.
- Host and mitochondria became metabolically integrated: neither could function normally without the other.
This event is often considered defining for the “last eukaryotic common ancestor” (LECA). All known eukaryotic lineages either:
- Have mitochondria, or
- Have organelles derived from mitochondria (e.g., hydrogenosomes, mitosomes) even if they no longer perform classical aerobic respiration.
This indicates that mitochondrial acquisition was an early, ancestral event rather than a later add‑on in a subset of eukaryotes.
3. Acquisition of plastids (chloroplasts and related organelles)
A second major endosymbiotic event produced plastids in a lineage of eukaryotes that already possessed mitochondria.
Primary plastids:
- Endosymbiont: a cyanobacterium capable of oxygenic photosynthesis.
- Host: a mitochondria‑containing eukaryote (probably a phagotrophic protist).
- Result: primary plastids with a double membrane, found today in three major groups:
- Glaucophytes
- Red algae
- Green algae and land plants
Mutual benefits:
- For the host:
- Access to photosynthesis: conversion of light energy into chemical energy.
- Autotrophic capacity—ability to produce organic compounds from CO$_2$.
- For the cyanobacterium:
- Stable, nutrient‑rich environment.
- Protection and potentially improved light access through host behavior (e.g., movement, position in the water column).
As with mitochondria, many cyanobacterial genes moved to the host nucleus. The resulting organelles:
- Are surrounded by two membranes (the former outer and inner bacterial membranes).
- Contain a reduced genome (the plastid genome).
- Depend on many nuclear‑encoded proteins that are imported into the plastid.
Secondary and tertiary plastids (briefly):
- In some lineages (e.g., many algae), a eukaryote already bearing a primary plastid was engulfed by another eukaryote.
- These events produced plastids with three or four membranes.
- Traces of the engulfed eukaryote can still be seen in some cases (e.g., a remnant nucleus called a nucleomorph).
- These more complex plastids represent additional rounds of endosymbiosis layered on top of the primary cyanobacterial event.
In the context of this chapter, the key point is that plastids show a second clear example of organelles originating from formerly free‑living prokaryotes.
Structural and molecular evidence for an endosymbiotic origin
Endosymbiotic theory is supported by multiple, independent types of evidence that point to a bacterial origin of mitochondria and plastids.
1. Double membranes and internal structures
Mitochondria and plastids typically have:
- An outer membrane similar in composition to the host’s outer membrane systems.
- An inner membrane with properties more typical of bacteria.
- Specific internal membrane folds or structures:
- Mitochondrial cristae (folds of the inner membrane).
- Thylakoid membranes in chloroplasts (sites of the light reactions of photosynthesis).
The two membranes fit an engulfment scenario:
- The inner membrane derives from the original bacterial plasma membrane.
- The outer membrane derives from the host’s membrane that surrounded the bacterium during phagocytosis.
2. Own DNA and circular genomes
Both mitochondria and plastids contain their own DNA:
- Organized into circular molecules, like typical bacterial chromosomes.
- Not packaged around histones in the same way as eukaryotic nuclear DNA (though there are variations and partial exceptions).
- Present in multiple copies per organelle.
This DNA encodes:
- A subset of the proteins needed for the organelle’s function.
- Its own rRNAs and tRNAs for organelle‑specific translation.
The presence of semi‑autonomous genomes strongly supports a former free‑living state.
3. Gene similarity and phylogenetic relationships
When sequences of mitochondrial and plastid genes are compared:
- Mitochondrial genes cluster with Alphaproteobacteria in phylogenetic trees.
- Plastid genes cluster with cyanobacteria.
This holds for:
- rRNA genes
- Many protein‑coding genes involved in respiration (mitochondria) and photosynthesis (plastids)
- Components of replication and translation machinery
Thus, molecular phylogeny directly links these organelles to bacterial groups, not to the host’s nuclear genome.
4. Bacterial‑like ribosomes and protein synthesis
Organellar ribosomes and translation apparatus show bacterial features:
- Mitochondria and plastids have 70S‑type ribosomes (with 50S and 30S subunits), typical of bacteria, rather than 80S cytosolic eukaryotic ribosomes.
- Their translation is sensitive to antibiotics that target bacterial ribosomes (such as chloramphenicol), but often less sensitive to those targeting eukaryotic cytosolic ribosomes (such as cycloheximide).
This functional similarity indicates that the organelle translation systems are directly inherited from bacteria.
5. Binary fission and independent replication
Mitochondria and plastids:
- Replicate by a process resembling bacterial binary fission.
- Have division machinery related to bacterial cell division proteins (e.g., FtsZ‑like proteins in some plastids and mitochondria).
- Do not form de novo; new organelles arise only from pre‑existing ones.
They are distributed to daughter cells during host cell division, but their replication cycle is regulated in coordination with the cell cycle, reflecting deep integration.
6. Gene transfer to the nucleus and metabolic integration
Over evolutionary time, many genes originally located in the endosymbiont genomes have:
- Been lost, or
- Been transferred to the host’s nuclear genome (a process called endosymbiotic gene transfer).
Consequences:
- Most proteins functioning in mitochondria and plastids are now encoded by nuclear genes.
- These proteins are synthesized in the cytosol and imported into the organelles via specific transport complexes in the organellar membranes.
This pattern:
- Explains why organelle genomes are so reduced.
- Demonstrates long‑term, intimate integration between host and endosymbiont.
- Supports the idea that organelles are no longer independent organisms but parts of a single, composite cell.
Evolutionary consequences of endosymbiosis
1. Energetic advantages and cellular complexity
The addition of mitochondria brought a large increase in available ATP per gene and per cell volume. Consequences:
- Energy‑intensive processes became feasible:
- Complex cytoskeleton and intracellular transport.
- Larger cell size.
- More elaborate gene regulation and signaling networks.
- This energetic “boost” is thought to have been a prerequisite for:
- The evolution of complex genomes with many noncoding regions.
- The origin of multicellularity and development of large, complex organisms.
In this view, mitochondria fundamentally changed the “energetic landscape” for eukaryotic evolution.
2. Expansion into new ecological niches
With mitochondria:
- Eukaryotes could exploit environments with higher oxygen levels.
- Some lineages adapted to anaerobic conditions by modifying mitochondria into hydrogenosomes or mitosomes, maintaining the basic endosymbiotic origin while shifting metabolic roles.
With plastids:
- Photosynthetic eukaryotes colonized sunlit environments on land and in water.
- These lineages became major primary producers, forming the base of many food webs and profoundly influencing global biogeochemical cycles (e.g., carbon and oxygen cycles).
Endosymbioses thus reshaped ecosystems and the biosphere.
3. Mosaic nature of eukaryotic genomes
Eukaryotic genomes are genetic mosaics:
- Archaeal‑like genes:
- Many components of information processing (replication, transcription, translation) resemble archaeal systems.
- Bacterial‑like genes:
- Many metabolic genes show bacterial affinities, especially from the mitochondrial and plastid lineages.
This mixture reflects:
- The archaeal host origin.
- Contributions of mitochondrial and plastid endosymbionts.
- Subsequent gene transfers among lineages (including from other bacteria and viruses).
Eukaryotes are, in this sense, chimeric organisms assembled through symbiosis and extensive gene exchange.
Extensions and open questions
1. Did endosymbiosis initiate or follow eukaryotic complexity?
Two broad perspectives exist:
- “Mitochondria‑early” views:
- Acquisition of the mitochondrial ancestor was a key trigger that enabled the development of full eukaryotic complexity.
- Many hallmark eukaryotic traits evolved after or during integration of the endosymbiont.
- “Mitochondria‑late” views:
- A proto‑eukaryote already had substantial complexity (cytoskeleton, endomembrane system, phagocytosis).
- Mitochondrial acquisition was a later step using already existing phagocytic abilities.
Current evidence (e.g., Asgard archaea features) suggests that the host had some complexity before endosymbiosis, but that mitochondria were acquired early in the path to full eukaryotic organization. The precise sequence of innovations remains an active research area.
2. Origin of other organelles and structures
While endosymbiotic origins of mitochondria and plastids are well supported, the status of other components is more uncertain:
- Nucleus:
- Most models propose an autogenous origin (from infoldings and specializations of host membranes) rather than a separate endosymbiont.
- Some speculative hypotheses suggest participation of symbiotic events, but direct evidence is limited.
- Peroxisomes and endomembrane system:
- Generally considered to arise from the host’s own membranes, not from endosymbionts.
- Cilia and flagella:
- Complex organelles likely evolved from host cell cytoskeletal systems, not by endosymbiosis.
Thus, endosymbiosis is central for mitochondria and plastids, but not a universal explanation for all eukaryotic structures.
3. Modern symbioses as analogues
Existing endosymbioses illustrate plausible intermediate stages on the way from free‑living bacteria to organelles:
- In some protists, internal cyanobacterium‑like symbionts perform photosynthesis but still retain many genes and partial independence.
- Some insects harbor intracellular bacteria (e.g., Buchnera in aphids) that supply essential nutrients:
- The bacteria have greatly reduced genomes.
- They are transmitted maternally, like mitochondria.
- They cannot live outside the host.
These examples show that stable, mutualistic endosymbioses can evolve and gradually tighten integration, suggesting how ancient events that produced mitochondria and plastids could have proceeded.
Summary of the endosymbiotic origin of eukaryotes
- An archaeal host cell ancestor entered into symbiosis with an Alphaproteobacterium, which became the mitochondrion.
- Later, a mitochondria‑bearing eukaryote engulfed a cyanobacterium, leading to plastids in some lineages.
- Multiple lines of evidence (double membranes, circular DNA, bacterial‑like ribosomes, phylogenetic relationships, organelle division, and gene transfer to the nucleus) support this origin.
- These endosymbiotic events were crucial for:
- The energetic capacity of eukaryotic cells.
- The evolution of eukaryotic complexity, multicellularity, and large body size.
- The rise of photosynthetic eukaryotes and major changes in Earth’s ecosystems and atmosphere.
The endosymbiotic theory thus explains not only how eukaryotic cells arose from prokaryotes but also why life on Earth is structured as it is today.