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Comment by jkhdigital | Hacker News Reader

> Intriguingly, all Borgs carry large FtsZ-tubulin homologs that may be involved in membrane remodeling or division, and proteins that resemble Major Vault Proteins and the TEP1-like TROVE domain protein that also do not occur in Methanoperedens genomes (Table S5). These are known to form the highly conserved and enigmatic eukaryotic vault organelle, a ribonucleoprotein that has been suggested to be involved in multidrug resistance, nucleo-cytoplasmic transport, mRNA localization, and innate immunity.

I can't follow most of this, but the phrase "highly conserved and enigmatic eukaryotic vault organelle" jumped out at me: https://en.wikipedia.org/wiki/Vault_(organelle)

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"Although vaults have been observed in many eukaryotic species, a few species do not appear to have the ribonucleoprotein. These include:

Arabidopsis thaliana

Caenorhabditis elegans

Drosophila melanogaster

Saccharomyces cerevisiae"

Wow. As if some hacker is playing against the researchers, removing the backdoor from all the most studied systems.

What do those organisms have in common that made them good model organisms that researchers favoured studying? Perhaps one of those same properties (fast reproductive rate, maybe?) requires ditching the vault complex.

Plausible. Makes one wonder what else we haven't figured out because of the same bias.

Arabidopsis thaliana is at least interesting because it tells time https://youtu.be/CA-YsWXRSHU?t=418

Really insightful comment. Thanks!

> Wow. As if some hacker is playing against the researchers, removing the backdoor from all the most studied systems.

Or perhaps it simply explains why it took so long to find them.

It's possible, although the cited articles in that section are from 1990 and 1991. (Another one links to a clone of the same wikipedia article in pfam, which is a comically circular reference.) We hadn't sequenced much then, so the absence of these organelles was probably established by microscopy in these model organisms.

The vault complex is an amazing enigma I’ve been following since finding the name while browsing through some gene lists. Every cell in our body has this massive complex, it’s highly conserved and we have not a clue what it does.

Even weirder, according to that Wikipedia article, it doesn't appear to be necessary, or has very non-obvious implications when it's removed. Yet, it's present in almost all eucaryote cells...

That is true for most things in the cell, though. There's an incredible amount of redundancy, optionality, and just plain unnecessary stuff. Vaults stick out because they're an apparently unnecessary thing that you can see down an electron microscope. There are many more equally unnecessary things that are just a lot smaller!

> and just plain unnecessary stuff

I'd like to point out that any protein that is produced takes up precious resources. Our evolutionary intuition suggests that unnecessary things should be dropped from the genome.

Suppose a protein is unnecessary. Then there would be no evolutionary pressure to keep it from mutating and loosing its function(and mutations happen all the time!). The organisms would just gradually loose it to mutations and we wouldn't find a conserved protein throughout eucaryotes. So there must be something keeping it.

Could it be a genetic parasite?

One conserved over the whole tree of life? That's like imagining an editing bug that Emacs and Vim have both carefully and inexplicably preserved from the last universal common text editor.

The genome is full of retrovirus remnants, so there’s a way for a parasite to piggyback on the host genome. Alu repeats in human genome are one such example. But there’s a hypothesis that these get “domesticated” by the genome and start serving a function.

Its well known what it does. The red pill activates it in 42% of all cells in your body and you wake up from your pod. Some people are known to surpass that threshold without taking a pill just reading HN comments. So be careful.

The favorite nucleoprotein offspring of the ribosome elder gods shall not be disturbed in their nursery, lest a wrath beyond mere animo-younglings' understanding shall be unleashed.

Anyone else stricken by how similar this looks to a flaggellar motor?

And, to my eye, not at all like a vaulted cathedral.

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