Not about everything

March 10, 2007

The beneficial prion, evolution and the origin of life

Filed under: biology,idea — takaita @ 23:01
Tags: , , ,

This article is speculating about evolution of species which is not based on changes in DNA.

Horizontal Gene Transfer
Currently, evolution is seen as DNA-based, because DNA is regarded as the only part of organisms that is inherited. DNA is the blueprint for an organism in the next generation. Richard Dawkins, in his book “The Selfish Gene” even shifted the focus of natural selection from complete genomes (species) to single genes. There is recently some unrest about Horizontal Gene Transfer (HTG, also called Lateral Gene Transfer). HTG is troubling, because it impacts our view of the tree of life. If genes are tranfered from one species to another, then the Tree of Life no longer has only branches (where species split of), but also knots (where the genome of different species are mixed to produce a new species).

Horizontal Gene Transfer is however not the only reason that the Tree of Life might have knots. There are researched cases of new species developed from hybridization of two other species, for example in the butterfly genus Heliconius and cichlids in Lake Tanganyika (fishes in East Africa).

The beneficial prion
A prion is an infectious protein. Some diseases are caused by prions, such as the Mad Cow Disease. A protein is a long chain of amino acids. Proteins can carry out their function in a cell because they have a special three-dimensional shape. Some proteins can be folded in different shapes. When such a protein has been folded differently, it will no longer be able to carry out the function it used to do. Prions are proteins that are shaped differently and also have the ability to refold other proteins into their own shape. The latter makes prions infectious. Once a single prion comes into a cell, it folds another protein. After finishing the job, there are two differently shaped proteins which each can fold another protein into their own shape. Then there are four, eight, sixteen etc of them.

It is interesting to notice that prions are self replicators. They require a very specific substrate which is only found in certain living cells.

Prions are usually a disease. They disturb the normal functionality of proteins and replace it with another (or no) functionality. That is what they have in common with mutations in the DNA, a change in a gene produces will produce a changed protein and only very rarely this protein has a beneficial effect on the organism. However these rare beneficial mutations in DNA are assumed to drive evolution.

Are there any beneficial prions? It is thinkable, and in fact there is an example of it. In yeast, a prion has been identified which in certain circumstances is beneficial, see for example Prions act as stepping stones in evolution. The remarkable thing is that the effect can be passed on to the offspring.

Inheritance of prions
It is important to notice that reproduction of organisms does not only involve the passing of DNA. Sexual reproduction involves an egg and a sperm cell. A sperm cell is assumed to be just DNA, encapsulated in machinery to transport the DNA into an egg. The egg however contains the complete machinery of a living cell: organels, proteins, ribosomes. That is needed because DNA on its own can not replicate, DNA on its own isn’t alive. DNA needs the machinery of a cell for reproduction.

A female who has acquired a beneficial prion might be able to pass this prion on to her offspring through the egg. And the offspring will then also pass this prion to the next generation. The prion is inherited.

There it is: a non-DNA-based mutation which is inherited.

Co-evolution of self-replicating systems
Continuing to speculate, I would like to consider living organisms not as just a machinery to replicate genes. This latter view, which has been promoted by Richard Dawkins in his book The Selfish Gene, seems too limited. There is more to an organism then just the manifestion of the information stored in the DNA. There is more inherited then just DNA.

There are several theories about the origin of life (I wish to ignore the creationist theories). They all agree on one point: it started with something able to self-replicate. In some theories that first thing is RNA. In other theories it is metabolism-first.

I like to think about the origin of life in terms of co-evolving self-replicating systems. There was RNA, there were bubbles of lipids, there were reaction chains (metabolism) and they all were self-replicating independently. RNA and reaction chains which would get into a bubble of lipids formed a self-replicating system and they co-evolved to living cells. The self-replication of each element became heavily dependent on the self-replication of the other elements. In the safety of the cell, RNA has partly been replaced by DNA.

A beneficial prion is a inheritable mutation in the metabolism-system, but not in the DNA-system. The different self-replicating subsystems of a living cell still have the possibility to evolve. Of course the DNA-based evolution is the most obvious. The blueprint model is the easiest to understand. It is the subsystem which has been subject to research when it comes to evolution.

What to research
I admit that there is a lot of speculation in the above. It needs research. And here are a few ideas for that. The trouble is that all living organisms are supposed to have evolved from a single common ancestor which already had evolved considerably. This Last Universal Common Ancestor (LUCA) must already have been pretty good at self-reproduction, because it outcompeted all rivals at the time. It must have had a well-developed integration of the different subsystems. What we should be looking for is examples of differences between species in the integration of the subsystems. Because we are facing the situation that all living organisms stem from this well-integrated LUCA, it is probably impossible to find a totally different way of integration. Although there is an exception: viruses. Viruses are not considered to be part of the LUCA ancestry. The origin of viruses is speculative.

The proteins of a metabolism-chain are currently seen as the result of DNA-based evolution. If they are the result of co-evolution between DNA and the metabolism-chains, then the metabolism-chains might have adapted to the DNA. As DNA (indirectly) produces proteins, some metabolism-chains might have changed to use available proteins. This opens the possibility that related metabolism-chains in different species rely on totally different genes. Are there any examples of this?

Are there more beneficial prions then the one found in yeast. Are there any proteins that act like prions, but are so beneficial that every member of a species has this prion.

Can viruses be considered as a different result of co-evolution of subsystems?

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7 Comments »

  1. Not that I’m impressed a lot, but this is a lot more than I expected when I stumpled upon a link on SU telling that the info is quite decent. Thanks.

    Comment by How to Get Six Pack Fast — April 15, 2009 @ 15:41 | Reply

  2. Sweet blog. I never know what I am going to come across next. I think you should do more posting as you have some pretty intelligent stuff to say.

    I’ll be watching you . 🙂

    Comment by PraxPlayclafe — June 4, 2009 @ 04:10 | Reply

  3. I’m frequently searching for recent infos in the WWW about this issue. Thankz!!

    Comment by endoptemo — December 12, 2009 @ 01:24 | Reply

  4. Could prion or similar unrelated transitional forms an indicator proof or missing link in the ongoing origin of life from the inorganic matter without any involvement of the living organisms or their metabolic processes in present day’s world? Is origin of life an ongoing continual process just not visible? Eventually life is important than the origin; but it is a great wonder why it originates or how it originates!!!!!

    Comment by andgbigbore — June 4, 2011 @ 17:26 | Reply

  5. Could it be that prion related dementia could have caused some of the unexplained human actions in the past? Is there any way known to science to detect the isomerlike misfolded proteins and selectively cause the to denature? Maybe like detect the mishape and use a co-factor to create a shape that a protease will selectively bind to causing the innappropriate prion to denature.

    Comment by James — March 31, 2012 @ 01:50 | Reply

  6. Just stumbled upon this. Do you have any more speculations along these lines?

    I am working on some of my own ideas about the origin of life. I hope to do more complete post on it but I have some inital speculations in this post.

    http://broadspeculations.com/2013/04/21/life-predates-earth/

    Comment by James Cross — July 21, 2013 @ 20:37 | Reply

    • Be sure to look into my last comment on the post I referenced.

      Comment by James Cross — July 21, 2013 @ 20:38 | Reply


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