Proteins in a boiling kettle? No worries.

One challenge in writing about basic evolutionary concepts is finding the balance between the creation of jargon-filled geek indulgences and the tedious rehashing of well-known facts and principles. Proteins are a case in point. Many readers will already know that proteins are the workhorses of life, nanomachines with finely-tuned functions and exquisite 3D structures to match. Many, I hope, already know that proteins are manufactured by reference to the famous genetic code, a universal DNA- and RNA-based system. Some perhaps know that proteins must be folded into those exquisite 3D structures, often with help from other proteins, in order to function. And one way to destroy a protein functionally, to cause it to unfold and perhaps even turn inside-out, is to heat it. We’re not talking about extreme heat (say, 500 degrees C as in a self-cleaning oven) that cooks everything down to carbon. We’re talking the kind of heat one finds in the kettle, or in bubbling hot springs in places like Yellowstone National Park in the US. Say, 95 degrees C.

Amazingly, there are life forms (aptly named ‘thermophiles’) that thrive in serious heat. The bacterium Thermus aquaticus is one of the best known—originally discovered in those Yellowstone hot springs, its DNA-copying protein made feasible decades of DNA copying in labs the world over, through a process called the polymerase chain reaction.

This is amazing because proteins in, well, normal organisms like us cannot tolerate 95 C. They unfold, and usually this is permanent. They don’t re-fold when the temperature goes back down. The process is called ‘denaturation.’ Cooking meat is a basic example of this. The heat denatures proteins, and essentially all of the denaturation is irreversible. The meat stays cooked. (Thank heaven. No one wants the haggis coming back to life.)

Somehow, then, the proteins in thermophiles like Thermus aquaticus have become super-stable. They refuse to unfold even when heated to near boiling. We should expect that natural selection, acting on the basic protein structure (the sequence of building blocks, which are amino acids), can hone the nanomachine into a heat-tolerating nanomachine.

TARDIS1This raises lots of interesting questions. Structurally, how does a protein get stabilized? And is this hard to do, or are there lots of options in the protein universe for evolution to choose from? A group of inventive biologists just published a paper asking those questions, in part using a biochemical approach reminiscent of a TARDIS. The group is led by Susan Marqusee at the University of California at Berkeley, and their article in PLoS Biology is Thermodynamic System Drift in Protein Evolution.

The group studied bacterial ribonuclease H1 (RNH) proteins, and started with two species: our old friend Escherichia coli, which prefers warm snug spots like human guts but is killed by boiling temperatures, and Thermus thermophilus, whose name leaves nothing to the imagination. The RNH proteins in these two species differ in their heat stability, as you would guess. The authors decided to study the evolutionary processes that led to these two different outcomes, by inferring the evolutionary changes that occurred in the deep past, then “resurrecting” those ancient proteins and studying them in the lab to see what they can do. (It would be fun to discuss how this works and to enthuse about the work of Joe Thornton, a coauthor with Marqusee and pioneer in this area of work, but Carl Zimmer has already done this all too well. Start here and follow the links. It’s worth it.)

The results are brilliant, and can be summarized very briefly as follows:

  • As expected, thermal stability seems to be maintained by natural selection.
  • Quite unexpectedly, the structural basis of this stability varies considerably.

That second point says something very interesting and important about protein evolution, or at least about the evolution of RNH proteins. It should be obvious that natural selection forces proteins to adopt appropriately stable forms. And it should be clear with some thought that selection has no power to enforce a specific solution. Marqusee and colleagues found that the proteins evolved to acquire the required stability but were noncommittal about how they achieved it. This means that there are lots of ways to solve the problem. And more importantly, it means that during the evolution of heat stability in RNH, the protein structures “explored” a large number of options. The authors wrote this in their abstract:

Thus, even while overall stability appears to be strongly driven by selection, the proteins explored a wide variety of mechanisms of stabilization, a phenomenon we call “thermodynamic system drift.” This suggests that even on lineages with strong selection to increase stability, proteins have wide latitude to explore sequence space, generating biophysical diversity and potentially opening new evolutionary pathways.

It seems to me to be a mistake to picture protein evolution as a nearly impossible search for a needle in a haystack. Proteins appear to be flexible and accommodating, even creative. Now if we could just get more people to follow their lead . . .

 

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