When did viruses/giruses evolve?

[MarkE]

You’ve probably heard of the RNA world hypothesis. Life started as as self-replicating single stranded RNA. Günter Wächtershäuser proposed that RNA cell membranes could have developed near black smokes. So there was autotrophic RNA as well as chemoautotrophic microbes (archaea) below the ocean in the Earth’s lithosphere, which is the home of these extremophiles, archaea, that show more metabolic similarities with eukaryotes than with bacteria.

Single stranded RNA with a membrane does remind of the structure of a viruses, so the question rises whether life started as a virus. Not all viruses have membranes. Were viruses the first free-living cells? Scientist Gustavo Caetano-Anolles and his colleagues at the University of Illinois reached another conclusion after pioneering a new way to map the microbial family tree. Viruses did not evolve first, they found. Instead, viruses and bacteria both descended from an ancient cellular life form. But while, like humans, like bacteria evolved to become more complex, viruses became simpler. Viruses have gradually shed genes they found they didn’t need, until they could no longer even reproduce on their own.

But how did viruses evolve? Complex organisms were simpler in the past, so how close are viruses related to archaea? Archaea show resemblances with eukaryotes, and 8% of our eukaryotic genome is made up of viral genes, but could some of those viral genes actually have been within us since that first sell-replicating RNA cell near black smokers? Could the phylogenetic tree be actually upside down, and instead of a common ancestor that split into bacteria on the left, and archaea/eukaryotes on the right, archaea and viruses were genetically much closer, and split into bacteria/eukaryotes? 

If viruses indeed didn't evolve first, does the conclusion of this research imply that giruses (giant viruses that don’t behave as metabolic limited as general viruses) went from complex structures to simpler ones….and back to complex structures again? Because that doesn't make a whole lot of sense to me.

Edited February 23, 2018 by MarkE

[CharonY]

I would take a step back and first try to establish whether the findings from Caetano-Anolles' group are a good representation of the evolutionary history. While interesting, their study was still speculative in nature (they fall under the broader area of the regression hypothesis that was rekindled by the findings of large protist viruses). Harish et al. have criticized some of the weaknesses of that particular study. However, the whole hypothesis is not firmly established. The more canonical view is still that of mobile genetic elements.

[StringJunky]

Here's a Nature article on the three main hypotheses,of which, CharonY has already mentioned one:

Quote

Where Did Viruses Come From?

There is much debate among virologists about this question. Three main hypotheses have been articulated: 1. The progressive, or escape, hypothesis states that viruses arose from genetic elements that gained the ability to move between cells; 2. the regressive, or reduction, hypothesis asserts that viruses are remnants of cellular organisms; and 3. the virus-first hypothesis states that viruses predate or coevolved with their current cellular hosts. https://www.nature.com/scitable/topicpage/the-origins-of-viruses-14398218

 

Edited February 23, 2018 by StringJunky

[Endy0816]

Probably a mix of all three.

[MarkE]

On 23/02/2018 at 5:22 PM, StringJunky said:

Here's a Nature article on the three main hypotheses,of which, CharonY has already mentioned one:

Thanks for the article. I really thought that the scientific community would know where viruses come from, since all the other organisms seem to have their place in cladistics. The RNA world hypothesis on the other hand is widely accepted. It doesn't seem too far-fetched to suggest that this single stranded RNA, at some point, must have developed a capsid, even though viruses without any protein coating (viroids) still exist.

Viruses do show activity, but whether this is intentional or not is hard to say. Influenza continuously mutates its genome (antigene drift). Animal flu viruses can mix with human flu virus to create a whole new hybrid (reassortment). The Mexican flu for instance was a combination of swine flu, bird flu and human flu. But is this happening spontaneously and preprogrammed? I really can't tell, but I'm not convinced yet that this is indeed the case. The absence of evidence is not the evidence of absence.

Edited February 26, 2018 by MarkE

[Endy0816]

They really appear to have come about multiple times, rather than all coming from one.

Animals we are closely related to or have domesticated, tend to be major sources of crossspecies ones.

Edited February 26, 2018 by Endy0816

[MarkE]

8 hours ago, Endy0816 said:

They really appear to have come about multiple times, rather than all coming from one.

Animals we are closely related to or have domesticated, tend to be major sources of crossspecies ones.

Do you mean that different viruses have evolved on different times in the past? That's an interesting idea. What virus are believed to be the most primitive? Is there some kind of chronological order we can derive by comparing the genome of all six virus classes?

[StringJunky]

53 minutes ago, MarkE said:

Do you mean that different viruses have evolved on different times in the past? That's an interesting idea. 

This quote is part of an argument why viruses do not represent lineages but includes a description of  what endy was saying. The information in the link is interesting

Quote

2. Viruses are polyphyletic

In a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors. Viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins. http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/

 

[MarkE]

1 hour ago, StringJunky said:

This quote is part of an argument why viruses do not represent lineages but includes a description of  what endy was saying. The information in the link is interesting

I don’t fully understand the apparently contradictory viewpoint of this article about whether viruses are alive or not. It states for instance the following: “The authors conclude that viral simplicity is a consequence of parasitism, not antiquity”. Well, parasitism, as far as I know, is always a form of life.

But in the end the article concludes that a virus is not alive. I can't really support this notion, at least not yet, because every virus consists of DNA or RNA, which is the most important property of life, and furthermore a virus, when it’s inside a cell, initiates a process with several sequential steps in order to replicate itself, which is the second most important property of life.

Are you, whatever their place on the evolutionary tree might be, convinced yet that viruses are not alive?

Edited February 26, 2018 by MarkE

[Strange]

22 minutes ago, MarkE said:

I don’t fully understand the apparently contradictory viewpoint of this article about whether viruses are alive or not.

I think it shows that "living" is not a binary thing. It is a spectrum. Viruses are "less alive" than plants or animals, and things like prions are even less alive.

[StringJunky]

1 hour ago, MarkE said:

I don’t fully understand the apparently contradictory viewpoint of this article about whether viruses are alive or not. It states for instance the following: “The authors conclude that viral simplicity is a consequence of parasitism, not antiquity”. Well, parasitism, as far as I know, is always a form of life.

But in the end the article concludes that a virus is not alive. I can't really support this notion, at least not yet, because every virus consists of DNA or RNA, which is the most important property of life, and furthermore a virus, when it’s inside a cell, initiates a process with several sequential steps in order to replicate itself, which is the second most important property of life.

Are you, whatever their place on the evolutionary tree might be, convinced yet that viruses are not alive?

But they don't  fullfil all the current criteria, which is arbitrary anyway and possibly subject to change at some point. Like Strange says, it's not likely binary. If you think about abiogenesis, that's not  a binary process either, so there is actually a precedent for things being on a continuum of classification from non-living to living, with viruses and prions somewhere in between.

Edited February 26, 2018 by StringJunky

[CharonY]

1 hour ago, MarkE said:

Well, parasitism, as far as I know, is always a form of life.

You are confusing it with metabolic parasitism, which is an important part of "normal" parasitism between living orgnaisms. However, here, we talk about genetic parasitism. I.e. viruses do not have a metabolism but hijack host mechanisms for replication of genetic material. However, the utter lack of metabolism as well as the fact that they are unable to replicate independently from a host (not due to nutritional constraints but by the lack protein producing faculties) makes most people consider them mobile genetic elements (simlar to transposons) rather than living organisms.

One way to circumvent the problem is that they originally were living, independent organisms and only lost it over time (regression hypothesis). 

[StringJunky]

7 minutes ago, CharonY said:

You are confusing it with metabolic parasitism, which is an important part of "normal" parasitism between living orgnaisms. However, here, we talk about genetic parasitism. I.e. viruses do not have a metabolism but hijack host mechanisms for replication of genetic material. However, the utter lack of metabolism as well as the fact that they are unable to replicate independently from a host (not due to nutritional constraints but by the lack protein producing faculties) makes most people consider them mobile genetic elements (simlar to transposons) rather than living organisms.

One way to circumvent the problem is that they originally were living, independent organisms and only lost it over time (regression hypothesis). 

Do you have a bias in favour of any of those ideas?

[CharonY]

Do you mean classification of viruses? The most conservative view is to look at them as mobile genetic elements. I.e. from the list you quoted earlier it would be consistent with point 1 and 3, the main difference there is that of timing. With the detection of giant viruses the regression hypothesis makes it harder to dismiss 2 outright. However, evidence is mostly indirect by nature and to me at least it is still very speculative.

If you mean the definition of living organism, I do agree that it is fuzzy. However functionally the inclusion of metabolism has been crucial to understand physiological properties. As such I would still view viruses in the same context as transposons, integrons, plasmids etc. If you come from the purely bioinformatic side or are a virus specialist, the view may be slightly different.

[StringJunky]

8 minutes ago, CharonY said:

Do you mean classification of viruses? The most conservative view is to look at them as mobile genetic elements. I.e. from the list you quoted earlier it would be consistent with point 1 and 3, the main difference there is that of timing. With the detection of giant viruses the regression hypothesis makes it harder to dismiss 2 outright. However, evidence is mostly indirect by nature and to me at least it is still very speculative.

If you mean the definition of living organism, I do agree that it is fuzzy. However functionally the inclusion of metabolism has been crucial to understand physiological properties. As such I would still view viruses in the same context as transposons, integrons, plasmids etc. If you come from the purely bioinformatic side or are a virus specialist, the view may be slightly different.

It was the first one. Cheers.

[CharonY]

Obviously I did not proofread. Hope it was somewhat understandable regardless.

[StringJunky]

6 minutes ago, CharonY said:

Obviously I did not proofread. Hope it was somewhat understandable regardless.

Both comments were useful.  

Edited February 26, 2018 by StringJunky

[MarkE]

On 2/26/2018 at 5:32 PM, CharonY said:

As such I would still view viruses in the same context as transposons, integrons, plasmids etc.

I would view viruses as pathogenic organisms. For instance, it's well known that helminths and protozoa (Toxoplasma Gondii, Dicrocoelium Dendriticum etc.) can manipulate their host by altering their behaviour. Bacteria in the gut are able to alter the neural signals in the vagus nerve. They can influence our decisions (what we eat) by releasing signalling molecules into our gut, and change our taste receptors. Well, a virus manipulates its host vector as well.

I did a little bit of research on the web and found out that there's a virus from the family Baculoviridae infecting moth and butterfly caterpillars, that incites them to eat incessantly providing nutrients that are needed for the virus's replication. When the virions are ready to leave the host, the caterpillar climbs high into a tree (which they would normally avoid, due to the risk of predators), until its cells are made to secrete enzymes that dissolve the caterpillar (yes, dissolves ), and the virus drips down onto leaves, which will be consumed by new hosts.

Therefore, I'm not sure if I can support your argument that viruses are merely genetic elements, rather than living organisms: 

On 2/26/2018 at 4:46 PM, CharonY said:

However, the utter lack of metabolism as well as the fact that they are unable to replicate independently from a host (not due to nutritional constraints but by the lack protein producing faculties) makes most people consider them mobile genetic elements (simlar to transposons) rather than living organisms.

Why aren't coding genes considered 'alive' anyway?

Edited March 29, 2018 by MarkE

[CharonY]

The parasitic part is not under question, the categorization as living organism is. 

51 minutes ago, MarkE said:

Why aren't coding genes considered 'alive' anyway?

Because a classification system  that puts a stretch of DNA into the same class as fully functional cells is not terribly useful.

[MarkE]

19 hours ago, CharonY said:

The parasitic part is not under question, the categorization as living organism is. 

Because a classification system  that puts a stretch of DNA into the same class as fully functional cells is not terribly useful.

Once it's inside a host, a virion behaves in a way we associate with life. And didn't all life originate from a (virion-like) RNA molecule? There's also the knowledge that influenza viruses manipulate humans into behaving more sociable, and make us sneeze to spread the virus even further.

Research has shown that endogenous retroviruses (that make up 8% of our genome) play a crucial role in the functioning of our brain. Among other things, hese viral sequences are able to regulate which genes are expressed. Mammalian cells have mechanisms to keep these genes silent by coating their DNA with molecules that suppress viral genes. However, despite this effort, the viral genes still manage to find a way to be switched on regardless. Scientists have discovered that in a multiple of different tumour cells, proteins had been produced by endogenous retroviruses.

I'm not convinced that viruses aren't at all related to living organisms in any way. They can deliberately influence a host in their own advantage, so to state that this is just some kind of glitch in nature, collateral damage that is coincidentally caused, can't be the whole story. If we can't change the definition of a virus, or a gene, in our current classification system, then perhaps we have to redefine the definition of life.

Edited March 30, 2018 by MarkE

[CharonY]

4 hours ago, MarkE said:

I'm not convinced that viruses aren't at all related to living organisms in any way.

You are kind of missing the main point here. Them considered not to be organisms is because of their total dependence on other metabolism. It is the opposite of not being related to them. Think about this: do you consider plasmids or transposons to be organisms? Why or why not?

[StringJunky]

All classifications are arbitrary and a set of criteria has been laid for what constitutes a living organism and viruses do not check off all the list

[MarkE]

@CharonY, do you support the eukaryogenesis hypothesis, which states that the eukaryotic cell nucleus is derived from a virus?

According to the viral eukaryogenesis hypothesis, the eukaryotic cell is a composite of three phylogenetically unrelated organisms: a viral lysogen that evolved into the nucleus, an archaeal cell that evolved into the eukaryotic cytoplasm, and an alpha-proteobacterium that evolved into the mitochondria.

A lysogenic helical virus with a bilipid envelope (such as the pox virus) bears a distinct resemblance to a highly simplified cellular nucleus (i.e., a DNA chromosome encapsulated within a lipid membrane.

What are your thoughts about this hypothesis?

[CharonY]

5 hours ago, MarkE said:

, do you support the eukaryogenesis hypothesis, which states that the eukaryotic cell nucleus is derived from a virus?

First thing you have to consider is that this hypothesis does not postulate that viruses were ever independent organisms and does not actually relate that much to your initial assumptions. Second, I see it as a possible hypothesis but it is not my actual research area and I have no strong assumptions regarding the origin of the nucleus. However, a more common assumption, lace the origin of the nucleus into the archaeal area, though AFAIK the issue is not resolved as of yet.

The fact that the eukaryotes are of mixed  arachaeal and bacterial origin, including the origins of plastids and mitochondria is pretty much the basic model (and taught as such in basic courses). But that has not direct impact on the role of viruses.

Now, what is actually interesting about giant viruses is that they  encode a translation machinery. That actually has opened up  the question whether they could have originated from another, now extinct cellular ancestor, and got reduced as an ancient adaptation to a parasitic life style. However some recent metagenomic studies suggest that the origins of these translation system are not from some sort of cellular ancestors, but that actually grabbed them via other viruses and through their respective hosts. That, in turn, is strong support against ancient origins from a cellular ancestor.

[MarkE]

17 hours ago, CharonY said:

However some recent metagenomic studies suggest that the origins of these translation system are not from some sort of cellular ancestors, but that actually grabbed them via other viruses and through their respective hosts.

That sounds interesting, I haven't heard of this study before. I'd like to learn more about this, could you provide any references/papers to this research? 

Edited April 6, 2018 by MarkE