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What was the ancestral eukaryote like?

lpetrich

lpetrich

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Eukaryotic cells are cells with true cellular nuclei. They have a lot of complexity that is lacking from most prokaryotes, and the evolution of that complexity continues to be a mystery. But we are gradually resolving that mystery.

An important clue is phylogeny. It can help resolve what the original eukaryote was like, by working from what is present and absent in each branch of the eukaryote family tree.

That could only be addressed in various hand-wavy fashion before sequencing of proteins and genes. Even there, there was a false start from the late 1980's to early 1990's: (early-branching protists, (animals, plants, fungi)). That was discovered to be due to a kind of artifact called long-branch attraction, and the phylogeny that emerged in the late 1990's has been pretty much stable for the last 20 years. In summary:
  • Amorphea / unikonts
    • Opisthokonta - animals, choanoflagellates, fungi
    • Amoebozoa - amoebas, slime molds
  • Diaphoretickes / bikonts
    • Archaeplastida - green algae (incl. land plants), red algae
    • SAR - Stramenopiles (diatoms, kelp, oomycetes, ...), Alveolata (ciliates, dinoflagellates, Plasmodium, ...), Rhizaria (foraminifera, radiolarians, ...)
  • Excavata - Discoba (euglena, trypanosomes, ...), Metamonada (Giardia, ...)
  • (lots of others that are difficult to place)
The Eukaryotic Tree of Life from a Global Phylogenomic Perspective
The Evolution of Multicellularity: A Minor Major Transition?
The revised classification of eukaryotes
Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group | Genome Biology and Evolution | Oxford Academic
Bacterial proteins pinpoint a single eukaryotic root | PNAS

The root of the eukaryotic family tree continues to be hard to determine. I've seen these hypotheses for the first eukaryotic branching:
Amorphea ... Diaphoretickes + Excavata
Amorphea + Diaphoretickes ... Excavata
Amorphea + Excavata ... Diaphoretickes
Archaeplastida ... all the others

Such contradictory hypotheses are a good indicator of difficult-to-resolve branching.
 
"What was the ancestral eukaryote like?"

Tastes like chicken, only smaller?

Seriously, I have never gotten clear on whether the appearance of eukaryotes represented a separate "start of life", or if they evolved/mutated from some prokaryotic form. And ah ain' ejamacated enough to read articles like those links and glean anything about that question. What can you tell me, lpetrich?
 
Now to features of this organism.

A very obvious inference is that it was one-celled. Multicellularity is scattered over eukaryotedom, with multicelled groups nestled in among one-celled organisms. Also, to the extent that they have been studied, details of multicellularity vary widely. So multicellularity evolved several times -- I've seen estimates like 20 or 25 times.

Mitochondria are almost universally found in eukaryotedom. Some protists instead have hydrogenosomes or mitosomes, but these are broken mitochondria. Some protists lack all such structures, but they sometimes still have mitochondria-related genes. So the ancestral eukaryote almost certainly had mitochondria. These structures are, in turn, most closely related to alpha-proteobacteria.

Chloroplasts' distribution is much more scattered. The ancestral chloroplast was a cyanobacterium likely acquired by the ancestor of Archaeplastida. However, many other eukaryotes do photosynthesis, and they do so with acquired green algae or red algae: "secondary endosymbiosis". So chloroplasts are *not* ancestral.

The nuclear membrane and nucleus-cytoplasm transport mechanisms.
Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. [Mol Cell Proteomics. 2009] - PubMed - NCBI
Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. [PLoS One. 2011] - PubMed - NCBI
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. [Cell Cycle. 2004] - PubMed - NCBI

The endomembrane system and its transport mechanisms. This system includes the the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes, and others. It does not include the membranes of mitochondria or chloroplasts.
First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes - ScienceDirect
Rab protein evolution and the history of the eukaryotic endomembrane system | SpringerLink
Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode. [J Cell Sci. 2007] - PubMed - NCBI
Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution. [Proc Natl Acad Sci U S A. 2008] - PubMed - NCBI

The cytoskeleton, a framework of protein strands:
The evolution of the cytoskeleton | JCB
Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton. [BMC Evol Biol. 2010] - PubMed - NCBI
Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era | BMC Evolutionary Biology | Full Text

Mitosis, the usual eukaryotic-cell division:
The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes. [BMC Evol Biol. 2011] - PubMed - NCBI

Meiosis, a part of the eukaryotic sexual cycle:
A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis. [Curr Biol. 2005] - PubMed - NCBI
An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. [PLoS One. 2007] - PubMed - NCBI
Conserved meiotic genes point to sex in the choanoflagellates. [J Eukaryot Microbiol. 2010 Jan-Feb] - PubMed - NCBI
Meiosis is directly known from Metazoa, Fungi, Archaeplastida, Stramenopiles, and Alveolata, and these papers discuss evidence of meiosis-related genes in organisms that have not been caught in the act. Trichomonas and Giardia are both excavates, meaning that meiosis has been observed all three of the highest-level large groups: Amorphea, Diaphoretickes, and Excavata.

In summary, the ancestral eukaryote was an organism with several complicated features that are lacking from most prokaryotes.
 
Elixir said:
"What was the ancestral eukaryote like?"

Tastes like chicken, only smaller?

Seriously, I have never gotten clear on whether the appearance of eukaryotes represented a separate "start of life", or if they evolved/mutated from some prokaryotic form. And ah ain' ejamacated enough to read articles like those links and glean anything about that question. What can you tell me, lpetrich?
Click to expand...
The evidence is pretty clear that eukaryotes evolved from prokaryotes. In fact, some prokaryotes (the Archaea) are more closely related to eukaryotes than to Bacteria. Here is a simple graphic showing one hypothesis for how this initially occured:

Evolution+of+Cell+Nucleus+and+ER.jpg


Peez
 
lpetrich said:
Now to features of this organism.

A very obvious inference is that it was one-celled. Multicellularity is scattered over eukaryotedom, with multicelled groups nestled in among one-celled organisms. Also, to the extent that they have been studied, details of multicellularity vary widely. So multicellularity evolved several times -- I've seen estimates like 20 or 25 times.

Mitochondria are almost universally found in eukaryotedom. Some protists instead have hydrogenosomes or mitosomes, but these are broken mitochondria. Some protists lack all such structures, but they sometimes still have mitochondria-related genes. So the ancestral eukaryote almost certainly had mitochondria. These structures are, in turn, most closely related to alpha-proteobacteria.

Chloroplasts' distribution is much more scattered. The ancestral chloroplast was a cyanobacterium likely acquired by the ancestor of Archaeplastida. However, many other eukaryotes do photosynthesis, and they do so with acquired green algae or red algae: "secondary endosymbiosis". So chloroplasts are *not* ancestral.

The nuclear membrane and nucleus-cytoplasm transport mechanisms.
Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. [Mol Cell Proteomics. 2009] - PubMed - NCBI
Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. [PLoS One. 2011] - PubMed - NCBI
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. [Cell Cycle. 2004] - PubMed - NCBI

The endomembrane system and its transport mechanisms. This system includes the the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes, and others. It does not include the membranes of mitochondria or chloroplasts.
First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes - ScienceDirect
Rab protein evolution and the history of the eukaryotic endomembrane system | SpringerLink
Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode. [J Cell Sci. 2007] - PubMed - NCBI
Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution. [Proc Natl Acad Sci U S A. 2008] - PubMed - NCBI

The cytoskeleton, a framework of protein strands:
The evolution of the cytoskeleton | JCB
Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton. [BMC Evol Biol. 2010] - PubMed - NCBI
Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era | BMC Evolutionary Biology | Full Text

Mitosis, the usual eukaryotic-cell division:
The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes. [BMC Evol Biol. 2011] - PubMed - NCBI

Meiosis, a part of the eukaryotic sexual cycle:
A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis. [Curr Biol. 2005] - PubMed - NCBI
An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. [PLoS One. 2007] - PubMed - NCBI
Conserved meiotic genes point to sex in the choanoflagellates. [J Eukaryot Microbiol. 2010 Jan-Feb] - PubMed - NCBI
Meiosis is directly known from Metazoa, Fungi, Archaeplastida, Stramenopiles, and Alveolata, and these papers discuss evidence of meiosis-related genes in organisms that have not been caught in the act. Trichomonas and Giardia are both excavates, meaning that meiosis has been observed all three of the highest-level large groups: Amorphea, Diaphoretickes, and Excavata.

In summary, the ancestral eukaryote was an organism with several complicated features that are lacking from most prokaryotes.
Click to expand...
It is perhaps dangerous to speak of "the" ancestral eukaryote, since the various features associated with eukaryotic cells almost certainly did not all evolve at once. For example, the evidence suggests that all living eukaryotic organisms can trace their ancestry to a cell with mitochondria, but it is quite possible that the earliest eukaryotic cells did not have mitochondria. It is even possible that some of the features now unique to Eukarya actually evolved in the prokaryotic ancestors of eukaryotes.

By definition the first eukaryote had a nuclear envelope, very likely with endoplasmic reticulum and possibly with other endomembrane system components. I would guess that the prokaryotic ancestor of the first eukaryotes had a well-developed cytoskeleton, allowing it to manipulate its membranes (this is what would have allowed it to evolve the endomembrane system, and engulf bacteria that could evolve into mitochondria). It is conceivable that early versions of mitochondria and mitosis (perhaps even meiosis, though that is perhaps a stretch) had already evolved before the nucleus, or they may have evolved later.

Modern eukaryotes certainly have several complicated features that are lacking from most modern prokaryotes, but it is not clear that this was the case for the earliest eukaryotes and prokaryotes.

Peez
 
Peez, it seems like you are talking about the organisms between the prokaryotes and the LECA, the Last Eukaryotic Common Ancestor. But the research that I've been discussing, research on eukaryote features, mostly gives us details of the LECA.

As I'd posted, the LECA had several distinctive eukaryote features. The eukaryote cell cycle is a haploid-diploid one:

Haploid: (X)
Haploid mitosis: (X) -> (XX) -> (X) + (X)
Cell fusion: (X) + (X) -> (XX)
Diploid: (XX)
Diploid mitosis: (XX) -> (XXXX) -> (XX) + (XX)
Meiosis: (XX) -> (XXXX) -> (XX) + (XX) -> (X) + (X) + (X) + (X)

Eukaryotic life cycles vary from mostly-haploid to part-haploid part-diploid to mostly-diploid. Plants do "alternation of generations" between multicellular haploid and diploid phases, though seed plants have reduced their haploid phases to only a few cells. Not as far as most animals and some algae: the haploid phase being one-celled.

Many protists, algae, and fungi have lookalike sexes or mating types: "isogamy". When they are not lookalikes, that is "anisogamy". An extreme form of it is differentiation into egg and sperm cells, "oogamy". From Nuclear condensation in protozoan gametes and the evolution of anisogamy - ScienceDirect, "The phylogenetic pattern of anisogamous species is consistent with multiple convergent gains of anisogamy," (from Google Scholar preview). So the LECA most likely had isogamy.

Mating types are known from fungi, ciliates (Amorphea), alveolates (Plasmodium falciparum and dinoflagellates), and stramenopiles (Phytophthora infestans) (Diaphoretickes) -- sometimes a large number of them.

So the LECA likely had mating types, presumably for avoiding inbreeding.
 
A mechanism of eating, phagocytosis, is widespread in eukaryotedom. It consists of pulling some prey into the cell and making a cell-membrane bubble around it. The cell then injects digestive enzymes into it and absorbs digested-cell molecules like amino acids and nucleotides. It then pushes that bubble to the cell membrane, releasing its contents to the outside: exocytosis.

The digestive enzymes themselves were likely originally used in proteasomes and exosomes, structures that recycle proteins and RNA molecules by cutting them up with digestive enzymes.

A modification of phagocytosis is external digestion, something that evolved separately in animals and fungi. This is releasing digestive enzymes into the actual exterior, rather than to cell-interior topological exteriors like the interiors of phagocytosis bubbles, proteasomes, and exosomes.

I did a literature search for where it is known to occur.

Animals:
PHAGOCYTOSIS IN FISH - ScienceDirect a chapter on a book called "Fish Immunology" -- "Phagocytosis, the cellular ingestion and digestion of particulate matter, is probably the most widely distributed defense reaction occurring in virtually all animal phyla." Or at least those that have been studied in any detail. Also, Functional genomic analysis of phagocytosis and identification of a Drosophila receptor for E. coli | Nature -- "The recognition and phagocytosis of microbes by macrophages is a principal aspect of innate immunity that is conserved from insects to humans. Drosophila melanogaster has circulating macrophages that phagocytose microbes similarly to mammalian macrophages1,2, suggesting that insect macrophages can be used as a model to study cell-mediated innate immunity."

I searched for mention of phagocytosis for several other much-studied species, and I found it all over the animal kingdom -- chickens, frogs, sea urchins, nematodes, snails, octopuses, and cnidarians.

Elsewhere:
Choanoflagellates, amoebas (Amoebozoa and some Excavata), dinoflagellates, ciliates, ...

A pitfall of this search was that I sometimes found discussions of what my search targets are subjected to, like parasites being subjected to phagocytosis by their hosts' cells.


So the LECA could likely do phagocytosis.
 
The fossil record is rather scanty for early eukaryotes. The oldest unambiguous one known is the red alga Bangiomorpha pubescens from 1200 Mya (1.2 billion years ago). It was identified as a red alga because if its abundant details. Its contemporaries include lots of organic microfossils called "acritarchs" because it is difficult to identify which present-day organisms are their closest relatives. Porter S. The fossil record of early eukaryotic diversification. Paleontol. Soc. Paper. 2004;10:35–50. has some details.

Plain spherical acritarchs start appearing around 1800 Mya, and "ornamented" ones around 1500 Mya. They do not have much variety at first, though they diversify around 800 Mya and roughly level off in the Ediacaran and Cambrian.

Testate amoebae in the Neoproterozoic Era: evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon | Paleobiology | Cambridge Core -- those are amoebas that make shells for themselves. Microscopic ones, of course.

Paleobiology of the Neoproterozoic Svanbergfjellet Formation, Spitsbergen around 750 - 700 Mya -- some green algae: Paleastrum (Chlorophyta, Chlorophyceae, Chlorococcales), Proterocladus (Chlorophyta, Ulvophyceae, Siphonocladales)

The second one of these has a weird feature: its cells do not completely divide, giving them multiple nuclei.

A Vaucheriacean Alga from the Middle Neoproterozoic of Spitsbergen: Implications for the Evolution of Proterozoic Eukaryotes and the Cambrian Explosion on JSTOR -- an alga much like Vaucheria (Stramenopiles, Xanthophyceae: yellow-green algae)

The Proterozoic Fossil Record of Heterotrophic Eukaryotes -- their oldest fossils are about 700 million years old. Author Susannah Porter speculates on why it is algae that have older fossils -- they don't eat other organisms, and thus they can more easily grow cell walls. Thus making them better-preserved.
 
I'd posted on a remarkable discovery in Eukaryote Missing Link? -- some Archaea microbes with lots of eukaryote-like features, or at least the genes for them.

In 2008, a team of oceanographers discovered some hydrothermal vents on the Mid-Atlantic Ridge in the Arctic Ocean, vents even farther north than their previous discovery of such vents around there in 2005. They used a remotely-controlled submarine to explore it, and they named it "Loki's Castle", after the Norse god associated with trickery and mischief, a reference to the difficulty of finding it. Also the castle-like appearance of the five vents there.

In 2010, someone took a core sample of the ocean-floor sediment from a nearby spot, and in 2015, some researchers worked out the genome of an organism from the genome fragments that they found in it. They named the organism Lokiarchaeum after where it was found and also that it was clearly a member of the Archaea branch of prokaryotes. It is not very close to any known organism, so it has gotten its own phylum, Lokiarchaeota. Since then, some similar genes have been discovered in other sediments, leading to naming of phyla Thorarchaeota, Odinarchaeota, and Heimdallarchaeota, after other Norse gods. They collectively form a group that has been named Asgard.

They have the honor of being the closest known prokaryotes to the eukaryote host cell, or at least the archaeal part of it.

I cannot help but be skeptical, because I'd like to see an actual organism growing and reproducing under laboratory conditions. That way one can get a better picture of how eukaryote-like it is.
 
lpetrich said:
Peez, it seems like you are talking about the organisms between the prokaryotes and the LECA, the Last Eukaryotic Common Ancestor. But the research that I've been discussing, research on eukaryote features, mostly gives us details of the LECA.

As I'd posted, the LECA had several distinctive eukaryote features. The eukaryote cell cycle is a haploid-diploid one:

Haploid: (X)
Haploid mitosis: (X) -> (XX) -> (X) + (X)
Cell fusion: (X) + (X) -> (XX)
Diploid: (XX)
Diploid mitosis: (XX) -> (XXXX) -> (XX) + (XX)
Meiosis: (XX) -> (XXXX) -> (XX) + (XX) -> (X) + (X) + (X) + (X)

Eukaryotic life cycles vary from mostly-haploid to part-haploid part-diploid to mostly-diploid. Plants do "alternation of generations" between multicellular haploid and diploid phases, though seed plants have reduced their haploid phases to only a few cells. Not as far as most animals and some algae: the haploid phase being one-celled.

Many protists, algae, and fungi have lookalike sexes or mating types: "isogamy". When they are not lookalikes, that is "anisogamy". An extreme form of it is differentiation into egg and sperm cells, "oogamy". From Nuclear condensation in protozoan gametes and the evolution of anisogamy - ScienceDirect, "The phylogenetic pattern of anisogamous species is consistent with multiple convergent gains of anisogamy," (from Google Scholar preview). So the LECA most likely had isogamy.

Mating types are known from fungi, ciliates (Amorphea), alveolates (Plasmodium falciparum and dinoflagellates), and stramenopiles (Phytophthora infestans) (Diaphoretickes) -- sometimes a large number of them.

So the LECA likely had mating types, presumably for avoiding inbreeding.
Click to expand...
I am familiar with this topic, but I was addressing the thread title ("What was the original eukaryote like?"), and this from the OP: "It can help resolve what the original eukaryote was like..." Thus I was addressing "the original eukaryote" rather than the Last Eukaryotic Common Ancestor, which had apparently evolved quite a few notable features.

Peez

- - - Updated - - -

lpetrich said:
A mechanism of eating, phagocytosis, is widespread in eukaryotedom. It consists of pulling some prey into the cell and making a cell-membrane bubble around it. The cell then injects digestive enzymes into it and absorbs digested-cell molecules like amino acids and nucleotides. It then pushes that bubble to the cell membrane, releasing its contents to the outside: exocytosis.

The digestive enzymes themselves were likely originally used in proteasomes and exosomes, structures that recycle proteins and RNA molecules by cutting them up with digestive enzymes.

A modification of phagocytosis is external digestion, something that evolved separately in animals and fungi. This is releasing digestive enzymes into the actual exterior, rather than to cell-interior topological exteriors like the interiors of phagocytosis bubbles, proteasomes, and exosomes.

I did a literature search for where it is known to occur.

Animals:
PHAGOCYTOSIS IN FISH - ScienceDirect a chapter on a book called "Fish Immunology" -- "Phagocytosis, the cellular ingestion and digestion of particulate matter, is probably the most widely distributed defense reaction occurring in virtually all animal phyla." Or at least those that have been studied in any detail. Also, Functional genomic analysis of phagocytosis and identification of a Drosophila receptor for E. coli | Nature -- "The recognition and phagocytosis of microbes by macrophages is a principal aspect of innate immunity that is conserved from insects to humans. Drosophila melanogaster has circulating macrophages that phagocytose microbes similarly to mammalian macrophages1,2, suggesting that insect macrophages can be used as a model to study cell-mediated innate immunity."

I searched for mention of phagocytosis for several other much-studied species, and I found it all over the animal kingdom -- chickens, frogs, sea urchins, nematodes, snails, octopuses, and cnidarians.

Elsewhere:
Choanoflagellates, amoebas (Amoebozoa and some Excavata), dinoflagellates, ciliates, ...

A pitfall of this search was that I sometimes found discussions of what my search targets are subjected to, like parasites being subjected to phagocytosis by their hosts' cells.


So the LECA could likely do phagocytosis.
Click to expand...
Agreed, and the evolution of the endomembrane system (and mitochondria) seem to have involved endocytosis/phagocytosis.

Peez
 
Asgard archaea illuminate the origin of eukaryotic cellular complexity and a review article, Archaea and the origin of eukaryotes

The second one has a history of our conceptions of archaeal phylogeny.

(Three domains) Bacteria, Archaea, Eukarya coequal, with Archaea = (Euryarchaeota, Crenarchaeota)
Bacteria, ((Cren, Eukarya), Eury)
Bacteria, ((TACK, Eukarya), Eury) where TACK includes Crenarchaeota
Bacteria, ((TACK, (Asgard, Eukarya)), Eury, DPANN)

That article also contains a diagram that shows which "eukaryotic signature proteins" are also present in which archaea.
  • Ribosomal ones (10): Asgard 6 - 9, TACK 3 - 8, Eury 4
  • Informational ones (6): Asgard 1.5 - 5, TACK 2.5 - 5, Eury 0.5
  • Membrane-trafficking machinery (11): Asgard 6 - 9.5, TACK 0 - 1, Eury 0
  • Cytoskeleton(5): Asgard 3 - 4, TACK 0 - 0.5, Eury 0
  • Ubiquitin system (7): Asgard 1 - 7, TACK 1 - 4, Eury 0

The review article also mentioned a continuing riddle of the origin of eukaryotes: their membrane lipids. Eucarya and Bacteria share fatty-acid ones, while Archaea have terpene ones. So if Eukarya originated from Archaea, then when did they switch from terpenes to fatty acids? I've seen the theory that it was the archaeon that was the first endosymbiont, and that it became the cell nucleus. A version of that is the "hydrogen hypothesis", where a bacterium released hydrogen and the archaeon consumed it.
 
Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes and Asgard archaea do not close the debate about the universal tree of life topology propose that their proximity to eukaryotes is due to contamination or horizontal gene transfer.

Asgard archaea are the closest prokaryotic relatives of eukaryotes rebuts them.

Genomes of Asgard archaea encode profilins that regulate actin | Nature, The eukaryotic ancestor shapes up -- "Asgard archaea are the closest known relatives of nucleus-bearing organisms called eukaryotes. A study indicates that these archaea have a dynamic network of actin protein — a trait thought of as eukaryote-specific."

Actin is a cytoskeleton protein that is involved in making cell parts move, like chromosomes in cell division. It is also what does the contraction in muscle cells.

A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree

Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic | Nature Ecology & Evolution
 
Oxygen and Sex | Proceedings of the Royal Society of London B: Biological Sciences -- proposes that Reactive Oxygen Species (ROS's) from mitochondrial metabolism induces many more mutations, and that the meiosis-fusion cell cycle emerged as a way of sorting out those mutations. Essentially random reshuffling, but with enough of it, one can get some combinations with fewer of the deleterious variants.

I recall that Eugene Koonin has proposed that the eukaryotic endomembrane system keeps the cell nucleus from getting swamped by genetic material from the organism's prey. It may also be good for keeping out troublesome ROS's.

-

Early photosynthetic eukaryotes inhabited low-salinity habitats | PNAS From character polarity, with the help of cyanobacteria and their character polarities. The ancestral cyanobacteria are also inferred to be freshwater organisms.

It only discussed Archaeplastida, those eukaryotes with a "primary endosymbiosis", with cyanobacterium-only chloroplasts. There are many other photosynthetic eukaryotes, but nearly all of them have a "secondary endosymbiosis", with "chloroplasts" that are one-celled eukaryotic algae. The only known exception is an organism called Paulinella, with a primary endosymbiosis.

A less technical account with a whimsical title: Hold the salt: Freshwater origin of primary plastids | PNAS
 
Now for eukaryote flagella (singular: flagellum). These are different in structure from prokaryote ones, and they have a characteristic 9+2 microstructure: 9 pairs of microtubules in a circle around 2 central ones (Eukaryotic Flagella: Variations in Form, Function, and Composition during Evolution | BioScience | Oxford Academic). Eukaryotes that have them usually have one or two of them, but some one-celled eukaryotes have a large number of them: ciliates, where they are called cilia (singular: cilium).

Let's see how they are distributed.  Flagellate has some big lists, and most eukaryotes do indeed have flagella. They are distributed across most of the major groups of them, and also in several difficult-to-place early branchers. There are some flagellum-less ones, like red algae, most fungi, and various amoeboid protists, and only some kinds of cells of many multicellular eukaryotes grow flagella, notably male gametes: sperm cells. But their widespread presence and shared architecture make one conclude that the LECA had a flagellum.
 
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