Friday, December 04, 2015

The Red and Black Queen- Hypothesis


I have so often talked about in this blog about the microbe-microbe interaction and often have presented with an idea on how there is a lot of competition with each species trying to get ahead of the other species. For example, Pseudomonas aeruginosa is a highly competitive organism and usually tries to dominate other species nearby, thereby providing a survival advantage. We often consider infections as uni-microbial in nature. It is my understanding that for the majority of the cases it does, but not always. In natural habitat polymicrobial act is a common feature.

Nature has a lot of examples of Multi-microbial interactions. Let us take well known examples of symbiosis. The tie up between the 2 organism is so unique that one doesn't survive without the other. An extreme case of this is endosymbiosis. One of the finest example, I recall is from an article called "Bug in a bug in a bug". The organism in discussion is Planococcus citri which has an endosymbiont- Tremblaya princeps which in turn harbours an endosymbiont of its own- Moranella endobia. Interestingly none of the can survive independently without the other. There are many such examples outside endosymbionts where organisms interdepend on each other for survival.

Illustration 1: The Red Queen Hypothesis.
“Now, HERE, you see, it takes all the running YOU can do,
to keep in the same place.” Source
Perhaps, everyone has heard of the Red Queen hypothesis. Its one of the most famous theories of evolution. The hypothesis states that for a species to survive it has to constantly evolve, which is just enough to stay in the competition for survival. There are books written on this concept. Let us take a quick simple example. Let us assume we have 2 bacterial species (X and Y) in a petri-dish, well mixed with an equal interest in proliferation. The survival advantage for both the species is kind of 50-50. By the course of mutation (Check my earlier posts here and here), let's say X is able to produce a bacteriocin which potentially attacks Y. Logically, Y evolves overtime a defence mechanism. X further evolves a counter defence mechanism and Y evolves a counter-counter defence mechanism. This process can infinitely loop out just to survive. There are extra genes and control mechanisms evolved by both species just to keep themselves in competition but the net effect is "Nothing". As good as each were at the start of competition. The more number of variables you add to this equation more complicated it gets but the idea will remain the same. There is no doubt as to if the above scenario is true, since this has experimentally demonstrated to be the case in a huge set of examples.

Illustration 2: Black Queen
Now think about this for a moment. If the two organism decide that they are not fighting each other, but rather share their work then each of them would get better share. Let us build another scenario with X and Y bacteria. X decides that it is going to do all the amino acid building stuff and Y decides that it will do all the lipid stuff (both in excess of requirement). So X is going to drop all those genes that is required to manage lipids and Y will drop of amino acid part. Once again the species are interlocked but in a symbiotic manner. X supplies its extra to Y and vice-versa. This has a special advantage, there is no competition to build genetic systems at an extra cost (Since you could drop some genes) which anyways is of little value over a longer period of time. This is the basis for Black queen hypothesis.

Black Queen Hypothesis, as per Morris etal; 2012 argues a theory on how organisms become dependent on each other. As Richard Losick comments "It's a sweeping hypothesis for how free-living microorganisms evolve to become dependent on each other. The heart of the hypothesis is that many genetic functions provide products that leak in and out of cells and hence become public goods". The idea is termed black queen to reflect the Heart- cards game where you need to have a minimum points to win. In microbial terms, you harbour minimum set of genes and still survive with the help of other. There is some mathematics in the original paper but let us ignore it here.

This airs a fresh new question. This theory looks ok when we talk about a couple of organisms involved. What happens to the scenario where one organism is helping a lot of others by taking up their function. This idea is well explained in the paper as "Shooting the moon strategy". Though it appears that this is a risky move for the universal helper (since it is the one that is doing everything needed), it can be a great move in ensuring survival. So even if such a helper is rare in the system, its survival will be ensured by others who are benefiting from the helper.

In summary, The Red queen hypothesis is a statement of competition while Black queen hypothesis is that of coordination.

Here is an interesting thought that I had been thinking about- Viral evolution. There is a huge debate on evolution of viruses. A great deal of scientists agree that viruses are involuted living organisms and another set of scientists argue that Viruses have evolved from chemical bags. I will present here some arguments from both sides and then come back to why I'm talking about it here.

First let us consider the argument that Viruses are previously living organisms that have lost multiple genes (If virus as we know it now are alive, is a totally different debate) . The idea goes something like this. Viruses where once intracellular parasites that had all the necessary genes for self replication. As evolution passed viruses relied more on the cellular machinery and started loosing genes, some of which was still available in host cell. The assumption in this argument is that loosing a gene is easier in comparison to gaining. Further, recent findings of viruses with very huge genomes is in support of this theory. It is argued that they lost a few genes. The other side of the argument is viruses are simple bag of chemicals that evolved to a certain extent and then found that it doesn't need to add up more genes since they could use it from host. One of the best arguments in this side of the prediction is viroids which can be simplified no further as a replication unit. The assumption here is gaining genes is quite easy. According to me we can avoid the assumption of timescale in both arguments since the evolutionary time that we are talking in each case is very high and thus will not effect our current observation. A good summation of the arguments is presented here.

It is commonly argued that virus follows the Red queen hypothesis. Virus competes with host for survival. This to me, is consistent with the idea that viruses have evolved from simpler chemicals. But if I consider that viruses have involuted, then it kind of looks like a negative black queen hypothesis. The virus must have started loosing genes as a mode of sharing but somewhere cheated, since it allowed them to replicate at a really low cost. And now has turned out to a Red queen strategy. Just a thought.
Morris JJ, Lenski RE, & Zinser ER (2012). The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio, 3 (2) PMID: 22448042

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