Giant viruses: gene capture or redundancy?

[mark!]

Is it more probable that giruses (giant viruses) acquired their cellular apparatus from another cell, or that they once were a functioning cell, but degraded over time, parasitizing other cells?

In the course of evolution viruses emerged many times. Viruses evolved on multiple, independent occasions by recruiting diverse host proteins that became major virion components. A small proportion (<1%) of the gene content of mimivirus is of host origin, many more genes (at least 25%) clearly link mimivirus to other large double-stranded DNA (dsDNA) viruses.

The same process explains the origin of the eukaryotic cell. Endosymbiosis explains how bacteria invaded an archaon, but the nucleus is, partly, of viral origin. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome (archaeon) and eventually usurping its role. A large poxvirus-like dsDNA virus might be at the origin of the eukaryotic nucleus, enclosed by an ancestral cell and adapted as an organelle. In some instances, RNA virus genomes undoubtedly captured cellular genes.

Megavirus, retained all of the genomic features unique to Mimivirus, in particular its genes encoding key-elements of the translation apparatus (seven aminoacyl-tRNA synthetases), a trademark of cellular organisms. It could suggest that large DNA viruses derived from an ancestral cellular genome by reductive evolution, which can be supported further by the presence of a large number of enzymes in genomes of giruses like various hydrolases, proteases, kinases, phosphatases and many others involved in cellular metabolic processes.

So have giant viruses degraded (just like mitochondria and chloroplast have lost the majority of their genes), or did they capture genes from a host? What's in your opinion more probable, and why?

 

[trurle]

Is it more probable that giruses (giant viruses) acquired their cellular apparatus from another cell, or that they once were a functioning cell, but degraded over time, parasitizing other cells?

I think the parasitic degradation evolutionary pathway is not likely. Even in mitochondria, the ribosomes and associated transport RNA machinery are persistent, while megaviruses and even pandoravirus absolutely lack ribosome-associated genes. More plausible explanation is what giant viruses never had ribosomes, and therefore never were an independent (cellular) life form.

From
https://academic.oup.com/femsre/article/39/6/779/550971

However, for cells living inside another cell, the existence of various compartments delimited by membranes (the cell nucleus on one side and the parasite membrane on the other), as well as regulatory incompatibilities between bacteria and eukaryotic subsystems, makes some functions more challenging to lose than others throughout reductive evolution. The impossibility to import ribosomes across a periplasmic membrane may be why the protein translation apparatus, in particular the ribosomes, are the last to be lost in all cellular parasites.

 

[mark!]

I think the parasitic degradation evolutionary pathway is not likely.

So they must have acquired those genes then.

But then the question remains: why/how would they acquire those genes?

 

[BillTre]

If that is what happened,
the genes were acquired by a randomly occurring process (probably when a virus infected a cell containing the genes).
The genes were then retained in evolution because it was adaptive in some way.

 

[mark!]

If that is what happened,
the genes were acquired by a randomly occurring process (probably when a virus infected a cell containing the genes).
The genes were then retained in evolution because it was adaptive in some way.

Interesting. Could you please elaborate more?

 

[jim mcnamara]

This article is about the origins of giant DNA virus and postulates that they arose before eukaryotic life became common (full article is behind a paywall), and possibly are the result the process of separating
processes that are now occur in the nucleus, from processes that occur in the cytoplasm:
https://www.sciencedirect.com/science/article/pii/B9780124081161000021

This broad phylogenetic distribution of hosts is consistent with the hypothesis that giant viruses originated prior to the radiation of the eukaryotic domain and/or might have been involved in the partition of nuclear versus cytoplasmic functions in ancestral cells.

It seems Giant DNA viruses arose separately from RNA viruses and probably at least concurrently with eukaryotes. AFAIK the only hosts for Giant viruses are eukaryotic organisms. They have double stranded DNA, which originates, we think, in plasmids of the Archaea:
https://ucmp.berkeley.edu/archaea/archaeamm.html

So Archaea may represent the LUCA of both Giant viruses and Eukaryotes.
LUCA - Last Universal Common Ancestor, see:
https://en.wikipedia.org/wiki/Last_universal_common_ancestor

 

[BillTre]

Interesting. Could you please elaborate more?

If their genes were acquired from somewhere, it would most likely be some cell it infected (very unlikely to be another virus I am guessing, however if two different viruses infected the same cell simultaneously, one could acquire DNA from the other).

In the universe of all such possible acquisitions of DNA sequences by giant viruses from cells, many would probably not be of any functional use to the virus. They would just be a burden for the virus to maintain those sequences over the generations. They would therefore have a negative adaptive value, and be at a selective disadvantage, and eventually go extinct.
On the other hand, if the genes had some functional use to the virus (who knows what?), then the viruses that had those sequences would be better adapted in some way then their contemporaries without the genes. They would be selected for and survive.

 

[trurle]

So they must have acquired those genes then.

But then the question remains: why/how would they acquire those genes?

It is an interesting question i have no clear answer. Evolutionary, must be an environment which was not energy or material deficient (or the energy expenditure for maintaining larger genome will result in negative selection). On the other hand, environment must be unstable enough in respect to availability of genes external to parasite, for instability to provide positive selction to aggregate more genes. My guess it is the environment of generalist parasite, depending on very wide spectrum of species. Counter-example of Rhabdoviruses which are generalist but yet small do exist though.

 

[mark!]

This article is about the origins of giant DNA virus and postulates that they arose before eukaryotic life became common

I can follow how they probably arose before eukaryotic cells, but I can't follow how they could have existed already before prokaryotic cells. So 'redundancy', in one way or another, must be part of the explanation here, instead of just gene capture/acquisition.

I mean, a giant virus, just like any other virus, needs a host to reproduce itself. It can't survive without a host. So therefore a virus could not have survived if there wouldn't be any host cells (with metabolic properties, such as ribosomes) around in the first place. You can't have bacteriophages without bacteria. Ergo, a (giant) virus could not have existed before a (prokaryotic) cell existed. Do you agree?