Scientists found a brand new branch of organisms in the boiling acid pools or Yellowstone National Park!
Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone Hot Springs
Before we had only found DNA viruses in these pools, DNA viruses infecting archaea.
Youngs troupe of scientists thought there might be more... but how do you find something if you dont know what you are looking for?
Well, with viruses we have some clues. There are some things viruses have that us 'normies' dont have. Like, RNA viruses need an RNA-dependent RNA polymerase to replicate. Us normie DNA creatures have no used for an RNA-RNA polymerase. Soooooo if one found a gene floating around that looked like it could code for one of those bad boys, you might have found a brand new RNA virus!
Thats exactly what Youngs group did, and thats exactly what they found!
We describe here identification of novel RNA viral genome segments from high temperature acidic hot springs in Yellowstone National Park, USA. These hot springs harbor low complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations directly isolated from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs.
What does this mean, though?
There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life, and in particular could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes.
... Collectively, our findings suggest the existence of novel positive-strand RNA viruses that likely replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.
These viruses are not just kinda new. They are really really different from the RNA viruses we already know about! NEW BRANCH OF VIRUSES! NEW BRANCH OF VIRUSES! YAAAAAY!!!
That red branch, the 'Contigs', doesnt cluster with any of the viruses we already knew about. NEEEEEEW!!! COOOOOL!!!
I'm surprised the RNA survives in that extreme heat, and no doubt in the presence of Ca2+ and Mg2+ ions as well.
Sweet - that's my next journal club contribution sorted.
I was too, which is why my first thought was contamination.
But amino acid comparisons of their sequences and known viruses showed patterns, but definitely distinct AA sequences for the RNA-RNA polymerase and gag proteins (Fig 4 and 5). We are not talking one AA here, one AA there different-- like, more different than similar, different.
Hell, even if it is contamination and the virus is not from the pools, they found something new.
Here's my prediction: the genome will be found to form strong secondary and teriary structures to enable it to avoid degradation.
Also, did the paper say whether the genome had an unusual amount of G an C residues? I couldn't see that anywhere. If so, it would be consistent with a genome that has evolved under thermophilic conditions.
Divalent cations are required for nucleases and DNA/RNA polymerases.
Also, RNA undergoes spontanous alkaline catalysed hydrolysis, and is therefore more stable in acidic medium.
Not being a biologist, much less a virologist, some of the graphical 'helping' aids confound me. Do you think in the future you could drop in subtle 'pst, look here' markers for people like me? Thanks in advance!
Yes. As shown best by Li and Breaker, the major determinants for (non-enzymatic) hydrolysis of RNA are high pH, presence of divalent cations, and high temperature. Though hydrolysis may be non-existent at acidic pH, many acidophiles actually maintain their cytoplasm at around neutral pH, so Li and Breaker's observation might still apply. As for the conditions inside the virus, that's an interesting future question.
They could still cluster near to and be new. Cluster is only a point of view.
a boiling pit of acid
Evil scientist with laboratory inside volcano is VINDICATED.
I've just enough science and engineering to be very dangerous to myself.
A little help, please, on the need for a "RNA polymerase"... what constitutes a polymerase in this context, how would it be available in these acidic conditions, and what pulls it into an RNA polymerase specifically?
Thanks for the very intruiging article.
Im'm not even suprised. I'm sure there are various form of life (although virus is not strictly alive) out there. Life is amazing.
I work with bacteria but would like a good intro into viral taxonomy. Could any of you suggest any good starting literature ?
Please write an article about:
Not having anything sensible to say about the science (unless "cool!" counts as sensible), I'll just keep my fingers crossed for Venusian viruses. Just imagine the alliterative headline possibilities.