Explaining how evolution can do the "impossible"

[wattsr1]

INTRODUCTION

This essay is my understanding of a paper titled “Evolution of Hormone-Receptor Complexity by Molecular Exploitation”.

It is based on the research paper at reference (1).

In order to try and simplify it, and make it more digestible, I am doing it largely in note form.

Given that the article is technical, this is my understanding only, and so should not be taken as a definitive representation of any of the reported research.

An excellent writeup, with diagrams can be found here:-

http://www.talkreason.org/articles/evo.cfm

and here:-

http://blogs.discovermagazine.com/lo...ind-locksmith/

Preference should go to these two links if there is any perceived conflict with my essay.


BACKGROUND

1. Mutation and selection have been shown to be able to create well adapted structures through a variety of studies - theoretical, in the laboratory, in the field and via simulations (e.g. Avida).

2. The mechanisms that assemble complex systems that depend on interacting components have not been so well demonstrated however.

3. For instance if A and B are two tightly interacting proteins then how can A evolve in the absence of B and vice versa. And if they evolve together, how can a change in one not kill off the effectiveness of the other. Simultaneous emergence of more than one part by mutation and selection is most unlikely. And so how these parts can arise and then link up is not so clear.

4. The functional interaction between the steroid hormone aldosterone and its specific receptor, the mineralocorticoid receptor (MR), is an example of this evolutionary puzzle.


IN THIS ESSAY

1. You will see a real example of the above kind of system, a classic molecular lock and key.

2. The essay will show how researchers determined a plausible path for the evolution of this system, by testing each part of that path in laboratory experiments.

3. You will see several classical evolutionary processes in action

a. gene duplication which allows one gene to explore while its partner maintains an original function.

b. complexity built up by using already existing components, but in new ways.

c. epistasis - whereby the interactions between genes allows only some viable pathways which result in the final outcome of the lock and key system.

4. The cumulative nature of science is on display. This research is built on preceding research and is informed by it, and reinforces it.


SOME TERMS

aldosterone
Aldosterone is a hormone (a protein which a cell uses to communicate with other cells). It stimulates the formation of messenger RNA involved in the formation of other proteins which are essential to transport of sodium and other ions around a cell. It’s a steroid hormone in that it can pass through the cellular membrane and bind to its receptor inside the cell, as against other hormones that can only bind to receptors on or in the cellular membrane.

mineralocorticoid receptor (MR)
Aldosterone is also known as a mineralocorticoid steroid. The receptor it binds to inside the cell is called a “mineralocorticoid receptor”. This hormone-receptor complex, once bound, then moves into the nucleus where it binds to a specific region of DNA, thereby directing the formation of messenger RNA, which is crucial to the formation of other proteins needed for the above mentioned ion regulation.

cortisol
A hormone which is activated by stress

glucocorticoid receptor (GR)
The receptor to which cortisol binds to in order to regulate metabolism, inflammation and immunity.

ligand
In this essay, a hormone. A ligand binding domain (LBD) is the place on a receptor where the hormone binds, thus activating it to carry out some function.


HOW DOES THE IMPOSSIBLE EVOLVE

The Problem

How can the functional interaction between aldosterone (a hormone) and its specific partner, the mineralocorticoid receptor (MR) evolve in a stepwise fashion? Both proteins need each other and so how can one get started when its partner does not exist? And once begun, how can either parter change without affecting the functionality of its mate?

Gene Duplication Again

The starting point was a gene duplication.

Earlier work (2) had shown that MR and a similar receptor, the glucocorticoid receptor (GR) had descended from a gene duplication, long ago, in the vertebrate lineage. Now they have different functions, and are activated by different hormones, MR by aldosterone and GR by cortisol.

However, while MR as activated specifically by aldosterone, it can be activated by cortisol, the same hormone that activates GR. (In MR expressing tissues, the presence of a cortisol clearing protein ensures that MR is only activated by aldosterone).

Determining then testing the kind of receptors were around prior to the duplication

To work out what happened for the MR/aldosterone interaction to evolve, the researchers (hereafter named “BCT”) reconstructed the ancestral corticoid receptor (AncCR) from which both GR and MR descended via gene duplication.

First they did some preliminary tests to “improve the robustness” of their inference about this AncCR.

-- they isolated corticoid receptor sequences from existing vertebrate taxa that have roots going right back to the beginnings of vertebrates (the jawless lamprey and hagfish).

-- they isolated GR and MR in an organism representing the next major stage in vertebrate evolution (the jawed, cartilaginous skate)

Phylogenetic analysis of these sequences indicated that the duplication leading to GR and MR occurred after the divergence of the jawless fish but before the split of the cartilaginous fish from the bony vertebrates (teleosts, the ray finned fish and the tetrapods, organisms with four limbs like us).

BCT tested these receptor sequences to see how they reacted to related hormone activators - aldosterone, cortisol, and 11-deoxycorticosterone (DOC).

-- the basal receptors were all activated by very low doses of all three hormones. That is the receptors were very sensitive to them.

-- this is the same as the behavior of MRs in teleosts and tetrapods.

-- only the GRs of tetrapods and teleosts were insensitive to aldosterone.

The initial hypothesis

The above findings indicated that before the duplication leading to GR and MR, the basal receptor, AncCR, could be activated by aldosterone (as well as the others). Only later did the GRs of the bony vertebrates lose their sensitivity to aldosterone.

Testing the initial hypothesis

The above hypothesis appeared a bit odd at first sight, because aldosterone is considered to be a tetrapod specific hormone. So why was an ancestral receptor sensitive to it given that it was not then around? In part, this turned out to be a clue to the evolution of the aldosterone/MR specificity.

To test this initial hypothesis, BCT used a technique called “gene resurrection” to characterize the ancestral corticoid receptor from which the initial duplication occurred. (Very briefly, this technique aligns either the DNA or the proteins from descendant species and works back towards the ancestor. Thus, if 10 alignments have lysine at a particular position, and 2 have arginine at that same position, then it is inferred that the direct ancestor also had lysine at that position. And so, step by step, computations are done back to the ancestral state at each position along a gene or at each position along a protein. In this particular case, they aligned protein sequences. A review article can be found at reference (3)).

They did not characterize the whole receptor, but only the part that constituted its functional portion, called the ligand binding domain (LBD).

They found that this LBD was “most similar to aldosterone-activated receptors MRs and CRs and differs from them by just one [amino acid] residue in the ligand-binding pocket”.

That is, their ancestral receptor turned out to be very similar in sequence to the modern aldosterone and corticoid receptors.

To see how it behaved, they made the DNA that made the LBD and put it into cultured cells to see what it was sensitive to. It indeed turned out to be sensitive to aldosterone, and like the CRs and MRs of existing organisms, was sensitive to DOC and to a lesser extent, cortisol.

By running a series of tests on different, but plausible AncCRs, they were able to demonstrate that their inference was robust to errors in their assumptions and associated computations.

Given this surprising ability of the AncCR to be activated by aldosterone (a molecule that had not yet evolved), BCT used sensitive techniques to see if the hormone happened to occur in very low concentrations within the plasma of lampreys and hagfish. If present then this could explain this sensitivity to aldosterone.

None could be found, using several tests, even though aldosterone is easily found across tetrapods but is absent in teleosts (ray finned fish), elasmobranchs (sharks, skates and rays) and agnathans (jawless fish - lampreys and hagfish).

From these tests it was clear that aldosterone is a relatively recent hormone, having arisen on the line leading to tetrapods. Other work (4 and 5) had shown that it arose from a modification of a molecule called “P-450 11B-hydroxylase”. This more ancient protein functions to hydroxylate (add hydroxyl ions to) DOC during a process known as glucocorticoid synthesis, which occurs in all jawed vertebrates. However, in tetrapods, the descendant of this molecule has taken on the additional function of hydroxylating corticosterone during the manufacture of aldosterone.

Hopefully by now you are beginning to see a pattern. The molecules involved here are not hopelessly different to each other. Duplications ensure the initial genes start off the same. Once one gene of the pair mutates, (leaving the other to maintain the original functionality), bits and pieces are already in place from existing systems, ready for a tweak here and there to be harnessed into the newly evolving system.

Given that the sensitivity of corticoid receptors to aldosterone actually predates the hormone itself, then something else must have been regulating AncCR. BCT proposed DOC, the hormone produced by the ancient and jawless lampreys and hagfish, and all jawed vertebrates such as sharks, ray finned fish and us, and which functions in the synthesis of other corticosteroids in these organisms.

Testing the hypothesis (DOC being the ancestral regulator)

Aldosterone differs from DOC in only two small areas of the protein and the experiments conducted by the researchers showed that neither of these affected activation of the existing or the ancestral corticoid receptors.

Because existing MRs essentially retain the ancestral structure, then the tight specificity between aldosterone and its MR must be due to a “secondary loss” of aldosterone binding in the GR. This is because both MR and GR began from a genome duplication of an ancient CR which was sensitive to DOC, and thus GR losing the ability to bind to aldosterone would have ensured its specificity with MR.

BCT explored the mechanism behind this functional shift. They found that two replacements on the AncCR produced a GR-like behavior. One was replacing Serine with Proline at position 106 on the AncCR, (S106P), and the other was replacing replacing Leucine with Glutamine at position 111, (L111Q).

With these two changes in place the required concentration of aldosterone required to activate the AncCR rose by three orders of magnitude, whereas moderate cortisol and DOC sensitivity were retained.

Other mutants used to locate the two required changes (S106P and L111P) showed no similar effect on AncCR.

They understood the reasoning for this effect given that other studies on humans had shown that these two residues (Proline and Glutamine) at their specific positions, affect the ligand binding site in such a way as to exclude aldosterone but enhance cortisol binding.

BCP then attempted to determine the order in which the two mutations occurred affecting the amino acid substitutions mentioned just above, thus leading to GR functionality.

They introduced each substitution on its own to the AncCR. Both were needed. If L111Q was the first mutation, then activation by all hormones was drastically reduced. However, when S106P was the first mutation, aldosterone and cortisol sensitivity was reduced but high DOC sensitivity was retained. Then, with L111Q as the second mutation, aldosterone sensitivity was further reduced while cortisol sensitivity was restored to its former value, characteristic of existing GRs.

BCT concluded that “[a] mutational path beginning with S106P followed by L111Q thus converts the ancestor to the modern GR phenotype by functional intermediate steps and is the most likely evolutionary scenario.”

The inferred process

The process they infer is as follows:-

1. The ancient corticoid receptor is activated by both DOC and cortisol.
2. It duplicates (one receptor will eventually become MR, the other GR).
3. Because it has duplicated, both DOC and cortisol activate both receptors.
4. The future MR receptor maintains a very similar structure to the original receptor.
5. It is preadapted to the evolution of aldosterone given the above and that aldosterone varies very little from DOC.
6. The future GR receptor mutates, thus cutting off activation by cortisol.
7. However DOC still activates it. (Cortisol can still activate the MR receptor)
8. The GR undergoes a second mutation, restoring cortisol activation
9. The DOC undergoes a mutation to aldosterone preventing its binding to GR but maintaining its binding to MR
10.The outcome? We have gone from one receptor (AncCR) being activated by two hormones (DOC and cortisol) to two receptors, each being activated by one hormone. MR is activated by aldosterone (it can be activated by cortisol, if present). GR is activated by cortisol only. It cannot be activated by aldosterone.

Their summary

Our findings demonstrate that the MR-aldosterone partnership evolved in a stepwise fashion consistent with Darwinian theory, but the functions being selected for changed over time. AncCR’s sensitivity to aldosterone was present before the hormone, a by-product of selective constraint on the receptor for activation by its native ligand. AncCR and its descendant genes were structurally preadapted for activation by aldosterone when that hormone evolved millions of years later. After the duplication that produced GR and MR, only two substitutions in the GR lineage were required to yield two receptors with distinct hormone-response profiles. The evolution of an MR that could be independently regulated by aldosterone enabled a more specific endocrine response, because it allowed electrolyte homeostasis to be controlled without also triggering the GR stress response and vice-versa.

BCT continue:-

This evolutionary scenario - recruiting an ancient receptor into partnership with a novel ligand - is the obverse of the dynamic previously established for the androgen and progestin receptors (AR, PR). In that case, duplicates of an ancient estrogen-responsive receptor evolved affinity for steroids that previously served as intermediates in estrogen synthesis. Together, the hormone-first history of AR and PR and the receptor first history of MR point to a general evolutionary dynamic: Novel interactions emerge when a newly generated molecule - usually a slight structural modification of duplicate of an existing one - recruits as a binding partner a more ancient molecule, which was previously constrained by selection for an entirely different function. This model, which we call “molecular exploitation”, is consistent with findings that other ancient biological features have been co-opted for novel functions.

And they continue:-

The puzzle that complex systems pose for Darwinian evolution depends on the premise that each part has no function - and therefore cannot be selected for - until the entire system is present. This puzzle might indeed cause Darwin’s theory to “break down” if the functions of the parts must remain static for all time. But virtually all molecules can and do participate in more than one process or interaction, so a complex’s elements may have been selected in the past for unrelated functions. Our work indicates that tightly integrated systems can be assembled by combining old molecules with different ancestral roles together with new ones ...

MY CONCLUSION

Not only do we see one well recognized process in action again, namely gene duplication, but we also see another effect that is becoming more understood and important in evolutionary studies - epistasis, or the effects of interactions amongst genes. Thus, in the example discussed here, the order in which the S106P and L111Q mutations occur is important to creating the specific GR functionality and ensuring that MR exists as and aldosterone only receptor.

What makes this kind of evolution so plausible, and hopefully the above essay shows it to some extent, is the constrained manner in which the evolution of a novel hormone/receptor system occurred. A gene duplicates allowing one of the pair to go exploring. The exploring is done within a family of related proteins - DOC, cortisone, aldosterone. Preadaption occurs by a new molecule retaining a very similar structure to other molecules. As the new system builds up, no where does it do anything wildly out of kilter with what is around it and what is available.



Regards, Roland


REFERENCES

(1) Jamie T. Bridgham, Sean M. Carroll, Josepht W. Thornton. “Evolution of Hormone-Receptor Complexity by Molecular Exploitation”, Science, 312 97-101, 7-Apr-2006.

(2) Joseph W. Thornton, “Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions”, PNAS, 98(10), 5671-5676

(3) Joseph W. Thornton, “Resurrecting ancient genes: experimental analysis of extinct molecules”, Nature Genetics 5, 366-375, May 2004.

(4) Yasuki Nonaka et al, “Frog cytochrome P-450 (11B,aldo), a single enzyme involved in the final steps of glucocorticoid and mineralocorticoid biosynthesis”, European Journal of Biochemistry, 229, 249-256, 1995

(5) Hannes E. Bulow and Rita Bernhardt, “Analysis of CYP11B gene family in guinea pig suggest the existence of a primordial CYP11B gene with aldosterone synthase activity”, European Journal of Biochemistry, 269, 3838-3846, 2002

[Catholicity]

interesting article....something else interesting about the P-450. Found in humans, apparently, some humans have it and some don't, and having it can tell whether or not certain medications can be broken down in the bodily system, www.mayoclinic.com

[wattsr1]

Here is another example to this kind of process in evolution, namely the exploitation of what is already in existence to go on and make something new, by grabbing a bit here and a bit there, changing functions slightly and stitching them together. However, this example operates at a higher level of complexity to the research I pointed out in the above essay. My essay dealt with new genes and new proteins. This example deals with a different system altogether, but one still based on interacting proteins.

Here is a picture of a fundamental cycle called the Krebs Cyble:-

http://www.uic.edu/classes/bios/bios.../krebsfull.htm

Looks pretty ugly huh?


Here is an explanation to the KC:-

http://en.wikipedia.org/wiki/Citric_acid_cycle


Note what Wiki says - “which is of central importance in all living cells that use oxygen as part of cellular respiration. “



Now here is an abstract to a 14 year old piece of research which showed a plausible way by which the cycle could have evolved:-

Meléndez-Hevia E, Waddell TG, Cascante M., “The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution.”, J Mol Evol. 1996 Sep;43(3):293-303.


The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.

Their research showed the same kind of thing. Lots of little subsystems doing other things in the cell, being harnessed and linked together to do something completely different.




Regards, Roland

[wattsr1]

I see that no YEC has explained why the above is not science, either.

[jordanriver]

I see that no YEC has explained why the above is not science, either.

sorry, didn't mean to strike a nerve....oops, sorry again because I just lied. I guess I did. I guess I am a fallable work in progress, Roland.
Your work is indeed science.

jr

[wattsr1]

sorry, didn't mean to strike a nerve....oops, sorry again because I just lied. I guess I did.

Naughty JR.

Nerves are o.k. though.

I guess I am a fallable work in progress, Roland.

Stick around. We'll straighten some rough edges out and have you adopting a more sensible approach to ToE and ancient earth in particular and science in general. You'll still end up a conservative Christian though. But that's o.k., even for an atheist like me.

Your work is indeed science.

jr

No, no JR. Not my essay. Rather, the research that the scientists did, showing through laboratory experiments, how aldosterone and its specific receptor possibly evolved following a genome duplication millions of years ago.

To my mind it's a nifty bit of research. It's a theme that comes up a lot these days. A gene duplicates. As soon as one of the pair mutates, the other is locked into maintaining the original genetic function. The mutated gene can then go on to explore a range of possibilities, most of which won't go anywhere. However, a few mutations lead to the picking up bits and pieces from surrounding systems and co-opting them into undertaking a novel function.

The research showed how this works for aldosterone/MR.


Regards, Roland

[jordanriver]

No, no JR. Not my essay. Rather, the research that the scientists did, showing through laboratory experiments, how aldosterone and its specific receptor possibly evolved following a genome duplication millions of years ago.

To my mind it's a nifty bit of research. It's a theme that comes up a lot these days. A gene duplicates. As soon as one of the pair mutates, the other is locked into maintaining the original genetic function. The mutated gene can then go on to explore a range of possibilities, most of which won't go anywhere. However, a few mutations lead to the picking up bits and pieces from surrounding systems and co-opting them into undertaking a novel function.

The research showed how this works for aldosterone/MR.

Regards, Roland

I have to concede the research is science whatever the motives of the researchers.
For some, the motive is to prove evolution works , therefore no supernatural magic is necessary.

For some others who might apply the same procedure but simply with a different motive, that being, 'look at the amazing machine Bible-Jesus designed. Lets study it and detail every working part to see if the parts are interchangeable in case the machine breaks down , then we can fix it, because helping repair broke-down people is the Christian thing after all'

jr

[wattsr1]

I have to concede the research is science whatever the motives of the researchers.

Good on you JR. (And you remain a deeply committed Christian).

For some, the motive is to prove evolution works , therefore no supernatural magic is necessary.

That's kind of like science in general. It has, over the centuries, offered natural explanations to things that were once explained by invoking the supernatural. See below.

Christian folk accept that is is so, but still remain Christian, even though they accept the natural explanation. They see is as a part of God's creation/revelation.

For some others who might apply the same procedure but simply with a different motive, that being, 'look at the amazing machine Bible-Jesus designed. Lets study it and detail every working part to see if the parts are interchangeable in case the machine breaks down , then we can fix it, because helping repair broke-down people is the Christian thing after all'

jr

You left out a third but very important class JR. Those who do it for a mixed motive. Francis Collins, ex head of the Human Genome Project probably did it for mixed motives. One, he thought the project would help us by knowing more about the human genome. Two, he thought we would learn more about human evolution. Collins is also a Christian. You also have folk like Robert Bakker (a pentecostal Christian IIRC). He is also a palaentologist who studies dinosaurs and accepts ToE in full. Presumably he does what he does, simply to learn more about how God did and does things.


Nearing time to prepare for work, too.


Regards, Roland