Microbes found that are the closest living relatives of complex cells

We can’t culture them, but their genes suggest a close relationship.

Read the whole story

 

[Z1ggy]

damn asgardians always messing with us.

 

[SolarMane]

So, what sort of genes do the residents of Asgard have?

Presumably, they have genes that let some of them fly around using magical hammers.

 

[muhname]

And, aside from the fact that they only grow in environments that lack oxygen, we have no idea of the sort of conditions they do like.

There are multiple near-complete genome assemblies for these guys now. To get an idea of what kind of stuff they like, all you have to do is to upload protein predictions to e.g. KEGG and go through the results (what energy/metabolic/etc. pathways are present). Also, I believe in the article they leaned toward the hypothesis that the major increase in complexity only came about when energy production was outsourced to the alphaproteobacterial symbionts (mitochondria).

 

[winwaed]

SolarMane[/url]":2s21uvl4]

So, what sort of genes do the residents of Asgard have?

Presumably, they have genes that let some of them fly around using magical hammers.

So Wranglers then (for magical hammer wrangling)

 

[miken32]

You've got an open <i> element

 

[adespoton]

miken32[/url]":1oxhf4br]You've got an open <i> element

Is that the fifth element?

 

[Whiner42]

To pull all of this together without actually isolating any organisms speaks to some pretty impressive science and technology!

 

[Chuckstar]

muhname[/url]":35ys0ec0]And, aside from the fact that they only grow in environments that lack oxygen, we have no idea of the sort of conditions they do like.

There are multiple near-complete genome assemblies for these guys now. To get an idea of what kind of stuff they like, all you have to do is to upload protein predictions to e.g. KEGG and go through the results (what energy/metabolic/etc. pathways are present). Also, I believe in the article they leaned toward the hypothesis that the major increase in complexity only came about when energy production was outsourced to the alphaproteobacterial symbionts (mitochondria).

Such predictions are only as good as our existing understanding of such extreme environments, how proteins operate in such environments, etc. Which is all pretty minimal.

 

[SunnyD]

The only criticism I have with the article is that it does a decent job doing the inverse, how eukaryota are similar enough to Asgard trying to make the case that eukaryotes are part of their lineage rather than a distinct group on their own, but it doesn't do enough to discuss how, exactly, the Asgardian archeota are different from eukaryota.

Other than that, one step closer to the origins of life I guess.

 

[Fatesrider]

adespoton[/url]":h5da9ex0]

miken32[/url]":h5da9ex0]You've got an open <i> element

Is that the fifth element?

I believe it's a trademarked product from Apple, hence why it can't be named.

 

[Torbjörn Larsson OM]

Ooo, I can name drop now! Thijs, the senior author on this and the earlier Lokiarchaeota paper, was a lecturer in my first regular genome biology course this fall. (I am back in school.)

The authors identified groups they termed Thorarchaeota, ...

I have not had time to read the paper, but I believe that group was named by Hug et al. in a recent metagenomic project [ http://meincmagazine.com/science/2016/04/ ... t-culture/ ].

The closest group to eukaryotes was Heimdallarchaeota, and it was found around Aarhus, Denmark, as I remember it from a quick peek into the paper. That is shallow waters, likely the harbor bottom. Close cousins! ;-)

 

[Torbjörn Larsson OM]

[Oops]

 

[Eurynom0s]

Z1ggy[/url]":2843xgoi]damn asgardians always messing with us.

I thought the other Asgard finally shut down Loki's abductions, though.

 

[dnjake]

The idea that mitochondria are the only big difference between eukaryotes and prokaryotes is nonsense. The idea that the evidence cited in this article is adequate to evaluate how close these archaea are to eukaryotes is nonsense. One obvious reality is that the distinction has to due with the word karyote. There is a very large difference in size between an eukaryotic cell and any prokaryotic cell that I have ever seen. Swallowing bacteria did not start with mitochondria or chloroplasts. It started with cells that swallowed bacteria for food. That kind of behavior is the root of the animal way of life. The word karyote has to do with having a nucleus. That nucleus is wrapped by the endoplasmic reticulum and contains multiple pairs of chromosomes. The ability to reliably divide those chromosomes and the nucleus during a cell division is another big common feature of eukaryotic cells. Sex is another major feature that allows eukaryotic organisms to efficiently explore a variety of genotypes even with the much slower life cycle that comes with the larger size of protozoan organisms. It is quite plausible that the evidence from studies of protein sequences could show that these archaea are the ancestors of eukaryotes. But unless these organisms are able to eat other prokaryotes, have multiple chromosome pairs, and have the chromosome mechanisms that are needed for sexual reproduction, there is a very large difference between them and any common protozoan organism.

 

[dnjake]

A quick looks at the article indicates that the presence of a number of key proteins to eukartyotic cell membrane trafficking and structure have been identified in these archaea. But the word histone does not seem to appear in the article at all. There does not appear to be any discussion at all related to chromosomes in the article and I did not see any measures of the size of these organisms. The protein evidence likely does indicate some kind of relationship with eukaryotic cells. But exactly what it is appears questionable. Yeast used to be considered very primitive eukaryotes. But, Yeast are now known to be closer to metazoan organisms then amoebae. It is just that Yeast have lost a large part of the common eukaryotic genome that is not needed for their way of life. It could be that these archaea are really some kind of descendant or cousin of eukaryotic cells that have managed somehow to pick up some of the DNA that is common to most eukaryotic genomes.

 

[crashworks]

Last year, a hydrothermal vent in the Arctic named Loki's Castle yielded organisms that picked up the name Lokiarchaea. Now, researchers have used Lokiarchaea's genome to find a large group of related species that they are naming the Asgard superphylum.

Ugh, scientists are such nerds.

 

[Cheesewhiz]

So they can't be cultured.

They must dig livin' the thug life...

 

[DarthSlack]

Whiner42[/url]":flsyzip5]To pull all of this together without actually isolating any organisms speaks to some pretty impressive science and technology!

It is impressive, but its actually been common practice for well over a decade now. What's changed more recently is the affordability (sequencing costs have fallen through the floor and are still falling) and compute power has skyrocketted AND become cheaper so you can analyze the terabytes and petabytes you get from sequencing.

Its a really interesting time to be in any sort of genomics because we're still in a perfect storm of increasing capabilities and decreasing costs.

 

[compagnied]

seems to have swallowed a bacteria, converted it to an energy-producing structure

Is this an allusion to the mitochondria?

 

[bthylafh]

compagnied[/url]":13y0cuat]

seems to have swallowed a bacteria, converted it to an energy-producing structure

Is this an allusion to the mitochondria?

Yes, yes it is.

 

[photochemsyn]

dnjake[/url]":7bq5tm97]. . . .It could be that these archaea are really some kind of descendant or cousin of eukaryotic cells that have managed somehow to pick up some of the DNA that is common to most eukaryotic genomes.

These phlyogenetic reconstructions are based mainly on the ribosome, which is an RNA scaffold with many associated proteins that converts nucleic acids into proteins. It's highly unlikely that these ribosomal genes could be horizontally transferred, and so they form the basis of the "tree of life phylogeny" of bacteria, archaea an eukaryotes, first described by Carl Woese c. 1990. Your views seems stuck back in the pre-1990 era, in other words.

So, by that basis, the Lokiarchaea are a member of the archaea, here's the original paper describing them.
http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html

Furthermore, nobody is claiming the only difference between the archael & bacterial vs. eukaryotic lineages is mitochondria. See for example perhaps the simplest free-living eukaryote:
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri, PNAS 2006

It has 20 chromosomes and very high gene density (8,166 protein-coding genes in 12.56 million base pairs), a single chloroplast and a single mitochondria. It's unclear whether it ever replicates sexually. Archaea in contrast have single circular chromosomes but with eukaryote-like transcription.

So this does give a picture of eukaryotic evolution in which archaea species, several billion years ago, (and which were probably poisoned by oxygen) incorporated bacteria which could scavenge oxygen (mitochondria), allowing them to survive in oxygenated environments, forming the basis of heterotropic eukaryotes, i.e. animals and fungi, and others also incorporated bacteria which could photosynthesize (chloroplasts) forming the basis of the green algae and plant lineages.

 

[Voyna i Mor]

photochemsyn[/url]":3nwdtkdt]

dnjake[/url]":3nwdtkdt]. . . .It could be that these archaea are really some kind of descendant or cousin of eukaryotic cells that have managed somehow to pick up some of the DNA that is common to most eukaryotic genomes.

These phlyogenetic reconstructions are based mainly on the ribosome, which is an RNA scaffold with many associated proteins that converts nucleic acids into proteins. It's highly unlikely that these ribosomal genes could be horizontally transferred, and so they form the basis of the "tree of life phylogeny" of bacteria, archaea an eukaryotes, first described by Carl Woese c. 1990. Your views seems stuck back in the pre-1990 era, in other words.

So, by that basis, the Lokiarchaea are a member of the archaea, here's the original paper describing them.
http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html

Furthermore, nobody is claiming the only difference between the archael & bacterial vs. eukaryotic lineages is mitochondria. See for example perhaps the simplest free-living eukaryote:
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri, PNAS 2006

It has 20 chromosomes and very high gene density (8,166 protein-coding genes in 12.56 million base pairs), a single chloroplast and a single mitochondria. It's unclear whether it ever replicates sexually. Archaea in contrast have single circular chromosomes but with eukaryote-like transcription.

So this does give a picture of eukaryotic evolution in which archaea species, several billion years ago, (and which were probably poisoned by oxygen) incorporated bacteria which could scavenge oxygen (mitochondria), allowing them to survive in oxygenated environments, forming the basis of heterotropic eukaryotes, i.e. animals and fungi, and others also incorporated bacteria which could photosynthesize (chloroplasts) forming the basis of the green algae and plant lineages.

Or: what no longer can kill me makes me stronger?

edit - pointless speculation deleted

 

[SixDegrees]

Voyna i Mor[/url]"o87pfnj]

photochemsyn[/url]"o87pfnj]

dnjake[/url]"o87pfnj]. . . .It could be that these archaea are really some kind of descendant or cousin of eukaryotic cells that have managed somehow to pick up some of the DNA that is common to most eukaryotic genomes.

These phlyogenetic reconstructions are based mainly on the ribosome, which is an RNA scaffold with many associated proteins that converts nucleic acids into proteins. It's highly unlikely that these ribosomal genes could be horizontally transferred, and so they form the basis of the "tree of life phylogeny" of bacteria, archaea an eukaryotes, first described by Carl Woese c. 1990. Your views seems stuck back in the pre-1990 era, in other words.

So, by that basis, the Lokiarchaea are a member of the archaea, here's the original paper describing them.
http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html

Furthermore, nobody is claiming the only difference between the archael & bacterial vs. eukaryotic lineages is mitochondria. See for example perhaps the simplest free-living eukaryote:
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri, PNAS 2006

It has 20 chromosomes and very high gene density (8,166 protein-coding genes in 12.56 million base pairs), a single chloroplast and a single mitochondria. It's unclear whether it ever replicates sexually. Archaea in contrast have single circular chromosomes but with eukaryote-like transcription.

So this does give a picture of eukaryotic evolution in which archaea species, several billion years ago, (and which were probably poisoned by oxygen) incorporated bacteria which could scavenge oxygen (mitochondria), allowing them to survive in oxygenated environments, forming the basis of heterotropic eukaryotes, i.e. animals and fungi, and others also incorporated bacteria which could photosynthesize (chloroplasts) forming the basis of the green algae and plant lineages.

Or: what no longer can kill me makes me stronger?

While astrobiologists have been looking for planets with temperatures in the Goldilocks zone and plenty of oxygen, it seems to be that life originated in high temperature oxygen free environments and then adapted as the planet changed. This implies that the probability of life out there could be a lot higher than is generally thought, and that planets that went through a different geological development could hold very, very different life forms.

The Goldilocks Zone is just the temperature range over which water remains in liquid form. All of these Archaea have been found in water, on earth.

I'm not aware that we've been seeking out life only on oxygen-bearing planets, given that we know free oxygen is a fairly recent byproduct of life itself, and that life got along just fine without it for billions of years.

 

[Phyllis Stein]

SolarMane[/url]":1n6m4lic]

So, what sort of genes do the residents of Asgard have?

Presumably, they have genes that let some of them fly around using magical hammers.

Naw.
Asgard was for the ordinary people.
Valhalla was for the Super Heroes.
(Valhalla translates to "The hall of the valiant".)

P.S.
The English language is a lot closer to the Viking language than some people think.
Tuesday,Wednesday,Thursday and Friday are named after Norse gods.

Wednesday= Wodin's day (Better known as Odin)
Thursday= Thor's Day.

 

[Phyllis Stein]

Archaea are by far the most primitive form of life.
Bacteria and Eukaryotes are much more advanced and complicated.
If we can figure out how the Archaea evolved we will be getting closer to finding out how DNA evolved.
In other words...we will be getting closer to the riddle of how life evolved.
P.S.
A virus is "half-life"
It is a bundle of RNA or DNA which uses "life" to replicate.
RNA and DNA viruses should also give us a clue about how life evolved in the first place though.

 

[SixDegrees]

Phyllis Stein[/url]":1jkaqxaa]Archaea are by far the most primitive form of life.
Bacteria and Eukaryotes are much more advanced and complicated.
If we can figure out how the Archaea evolved we will be getting closer to finding out how DNA evolved.
In other words...we will be getting closer to the riddle of how life evolved.
P.S.
A virus is "half-life"
It is a bundle of RNA or DNA which uses "life" to replicate.
RNA and DNA viruses should also give us a clue about how life evolved in the first place though.

Uh, no.

 

[ratpH1nk]

dnjake[/url]":1q82w6ol]The idea that mitochondria are the only big difference between eukaryotes and prokaryotes is nonsense. The idea that the evidence cited in this article is adequate to evaluate how close these archaea are to eukaryotes is nonsense. One obvious reality is that the distinction has to due with the word karyote. There is a very large difference in size between an eukaryotic cell and any prokaryotic cell that I have ever seen. Swallowing bacteria did not start with mitochondria or chloroplasts. It started with cells that swallowed bacteria for food. That kind of behavior is the root of the animal way of life. The word karyote has to do with having a nucleus. That nucleus is wrapped by the endoplasmic reticulum and contains multiple pairs of chromosomes. The ability to reliably divide those chromosomes and the nucleus during a cell division is another big common feature of eukaryotic cells. Sex is another major feature that allows eukaryotic organisms to efficiently explore a variety of genotypes even with the much slower life cycle that comes with the larger size of protozoan organisms. It is quite plausible that the evidence from studies of protein sequences could show that these archaea are the ancestors of eukaryotes. But unless these organisms are able to eat other prokaryotes, have multiple chromosome pairs, and have the chromosome mechanisms that are needed for sexual reproduction, there is a very large difference between them and any common protozoan organism.

Not sure what all of the down voting. The lost me on the first sentence that, IMO for a "nerdy" science article should have read:

Thanks to microscopy, early biologists were able to make a binary distinction: there were eukaryotes and prokaryotes.

 

[Voyna i Mor]

ratpH1nk[/url]":2km3vge2]

dnjake[/url]":2km3vge2]The idea that mitochondria are the only big difference between eukaryotes and prokaryotes is nonsense. The idea that the evidence cited in this article is adequate to evaluate how close these archaea are to eukaryotes is nonsense. One obvious reality is that the distinction has to due with the word karyote. There is a very large difference in size between an eukaryotic cell and any prokaryotic cell that I have ever seen. Swallowing bacteria did not start with mitochondria or chloroplasts. It started with cells that swallowed bacteria for food. That kind of behavior is the root of the animal way of life. The word karyote has to do with having a nucleus. That nucleus is wrapped by the endoplasmic reticulum and contains multiple pairs of chromosomes. The ability to reliably divide those chromosomes and the nucleus during a cell division is another big common feature of eukaryotic cells. Sex is another major feature that allows eukaryotic organisms to efficiently explore a variety of genotypes even with the much slower life cycle that comes with the larger size of protozoan organisms. It is quite plausible that the evidence from studies of protein sequences could show that these archaea are the ancestors of eukaryotes. But unless these organisms are able to eat other prokaryotes, have multiple chromosome pairs, and have the chromosome mechanisms that are needed for sexual reproduction, there is a very large difference between them and any common protozoan organism.

Not sure what all of the down voting. The lost me on the first sentence that, IMO for a "nerdy" science article should have read:

Thanks to microscopy, early biologists were able to make a binary distinction: there were eukaryotes and prokaryotes.

It would seem that you didn't read the article, and that history of science is not your forté.

Early cellular biologists divided like into eukaryotes and bacteria exactly as the article said - with bacteria including the cyanobacteria. **Subsequently** nucleus-lacking organisms were identified which were not bacteria and the kingdom of archaea was introduced to hold them. The article explains this. You seem to anxious to put other people down - e.g. your unhelpful post "uh, no" above - that you manage to achieve a comprehension fail yourself.

 

[ChiralMichael]

compagnied[/url]":3lff3ken]

seems to have swallowed a bacteria, converted it to an energy-producing structure

Is this an allusion to the mitochondria?

It's an allusion to your mom.

......

What? That's where you get your mitochondria from.

 

[mcswell]

Thanks to microscopy, early biologists were able to make a binary distinction: there were eukaryotes and prokaryotes.

I was about to say that when I studied biology (1960s), blue-green algae (without nuclei, and now called cyanobacteria) were lumped together with other algae (with nuclei), I guess on the basis of both groups using chlorophyll for photosynthesis. I must be mis-remembering...