Evolution of alcohol synthesis

i-ccbc028bf567ec6e49f3b515a2c4c149-old_pharyngula.gif

We need to appreciate beer more. Alcohol has a long history in human affairs, and has been important in purifying and preserving food and drink, and in making our parties livelier. We owe it all to a tiny little microorganism, Saccharomyces cerevisiae, which converts complex plant sugars into smaller, simpler, more socially potent molecules of ethanol. This is a remarkable process that seems to be entirely to our benefit (it has even been argued that beer is proof of the existence of God*), but recent research has shown that the little buggers do it all entirely for their own selfish reasons, and they've been busily making alcohol that has gone undrunk by humankind for tens of millions of years.

In order to explain how we know this, forgive me, but I must explain some very basic biochemistry, and summarize what cells do to extract energy from sugar. We start with a 6 carbon sugar molecule. As a first step, called glycolysis, enzymes in the cell snap the molecule in half, liberating a little bit of energy and producing two 3-carbon molecules, called pyruvate.

Pyruvate gets passed on to the next step, called the citric acid cycle. This is a series of reactions that breaks the 3-carbon chain down carbon by carbon, liberating yet more energy at each step. It's all the steps after glycolysis that extract the bulk of the energy from the sugar molecule, but there's a catch: these steps require oxygen to run (this is also called the aerobic pathway). No oxygen, no citric acid cycle. Glycolysis can run, but some of the reaction products (especially a compound called NADH) accumulate, and soon enough that reaction would get choked off, too.

In the absence of oxygen, cells can continue to get that little bit of energy from glycolysis if only they can get rid of the accumulating reaction products somehow. In us, our cells do that by carrying out an additional reaction to convert excess pyruvate and NADH to another 3-carbon molecule, lactate, and NAD+. Lactate diffuses out of the cells and into the blood stream, forming lactic acid. When you are exercising anaerobically, that is, making your cells work harder than you can deliver oxygen to them, they limp along by dumping 3-carbon molecules in the form of lactic acid so they can keep burning sugar inefficiently. Once you're done working out, and your oxygen intake catches up, the lactate is converted back to pyruvate and can be burned completely and efficiently in the citric acid cycle.

Yeast do something different. If they are under anaerobic conditions, say, deep in the flesh of some decaying fruit, or in a wine bottle, they have the same problem: they want to keep their metabolism going by carrying out glycolysis, but to do that they have to get rid of accumulating products, somehow. They don't do it by making lactic acid, though (thank goodness—if they did, fermentation would produce a vinegary acid). Instead, they take the 3-carbon pyruvate and split off one carbon, producing CO2, which is given off as a gas. Any homebrew beer makers out there will be familiar with the idea of monitoring fermentation by observing the gas being produced.

The 2-carbon molecule left behind is called acetaldehyde. Acetaldehyde is further processed by an enzyme called alcohol dehydrogenase, Adh for short, which also recycles NADH. Adh converts the 2-carbon acetaldehyde into another 2-carbon molecule, ethanol. Alcohol. Booze.

Just like us, yeast produce this byproduct to keep going under anaerobic conditions, and when oxygen is available, they try to recover the energy in the alcohol. Familiar brewers' yeast has two forms of alcohol dehydrogenase: Adh1, which favors the production of alcohol from acetaldehyde, and Adh2, which more effectively runs the reaction in reverse, producing acetaldehyde from alcohol, and allowing the 2-carbon molecule to be fed back into the citric acid cycle.

If you'd rather see this in a simple biochemical diagram of the yeast pathways, click on the picture below: it says the same thing I just wrote up there.

i-15ec48b73092e63f0ef24917c72b511a-yeast_adh_sm.gif
Enzymes in red are associated with gene duplications that, according to the transition redundant exchange clock, arose nearly contemporaneously. The make-accumulate-consume pathway is boxed. The shunting of the carbon atoms from pyruvate into (and then out of, blue arrows) ethanol is energy-expensive, consuming a molecule of ATP (green) for every molecule of ethanol generated. This ATP is not consumed if pyruvate is oxidatively decarboxylated directly to acetyl-coenzyme A to enter the citric acid cycle directly (dashed arrow to the right). If dioxygen is available, the recycling of NADH does not need the acetaldehyde-to-ethanol reduction.

The yeast method of handling anaerobic conditions is not particularly efficient. They have to burn a little extra energy to prepare acetaldehyde for the citric acid cycle (the steps in green in the diagram above), which wouldn't be necessary if they used a 3-carbon intermediate as we do. So, one question is why they use a relatively inefficient method to carry out anaerobic metabolism.

One explanation is that humans are responsible—we've been selecting for yeast that produce intoxicating byproducts. A prediction from that would be that alcohol production would be a relatively recent innovation. An alternative explanation is that yeast have been doing this as a clever strategy—flooding their environment with a poison that that they can tolerate but that other microorganisms cannot is a way to limit competition for resources. A prediction from this is that the yeast evolved first to produce ethanol, and only secondarily evolved the ability to recycle it. A recent study strongly supports the latter hypothesis.

First, molecular clock analysis of various yeasts suggests that the ethanol enzymes began to diversify about 80 million years ago…at about the time flowering plants started producing fleshy fruits (that meteor at the end of the Cretaceous may have had an abrupt impact on the lives of dinosaurs, but I wonder if the explosion of flowering plant species before that may have had an equally profound, if more drawn out, effect). Face it, people, the chemistry of beer is for the benefit of yeast, and didn't evolve for our enjoyment. Or if it were the result of domestication, it was by the undiscovered species Zymurgosaurus dipsomanius, not Homo sapiens.

The second line of evidence is very cool. It would be instructive to be able to directly examine the metabolism of yeast from 80 million years ago, and measure for ourselves the activity of their Adh enzyme. We don't have a time machine, unfortunately, but we do have the ability to reconstruct ancient genes.

The authors compared the sequences of Adh1 and Adh2 from S. cerevesiae and from 15 other Adh homologs in other yeast species. They then calculated the maximum likelihood gene sequence for the last common ancestor of these enzymes, the primordial alcohol enzyme, which they called AdhA. They then took modern yeast, removed their Adh1 and Adh2 genes, and replaced them with AdhA. Voilà, they have yeast from the Age of the Dinosaurs.

They then analyzed the chemical kinetics of this enzyme. The question was whether it was more like Adh1, the enzyme that primarily makes ethanol, or whether it was more like Adh2, the enzyme that primarily consumes alcohol. Did yeast evolve this enzyme to make a byproduct to inhibit its competitors, or did it evolve it to eat this byproduct?

The answer is that it was more like Adh1, and that early yeast were brewers, not drinkers.

Notably, the kinetic properties of the remaining ancestral AdhA candidates resembled those of Adh1 more than those of Adh2. From this, we inferred that the ancestral yeast did not have an Adh specialized for the consumption of ethanol, similar to modern Adh2, but rather had an Adh specialized for making ethanol, similar to modern Adh1. This suggests that before the Adh1-Adh2 duplication, the ancestral yeast did not consume ethanol. This implies that the ancestral yeast also did not accumulate ethanol under aerobic conditions for future consumption and that the make-accumulate-consume strategy emerged after Adh1 and Adh2 diverged. These interpretations are robust with respect to the ambiguities in the reconstructions.

We can assemble a history of yeast fermentation from this information now. The first step was the gradual evolution of efficient alcohol-producing enzymes that allowed the yeast to colonize and exploit rotting fruit exclusively. This occurred a very long time ago, in the Cretaceous. Next, there was a gene duplication event that produced two copies of Adh; initially, both would have done exactly the same thing, just allowing the lucky duplicators to pump out alcohol even faster. With two copies, though, one would have more freedom to drift and change its enzymatic properties without serious consequence to the owner. One fortuitous change would be a shift in enzyme kinetics in one copy to better promote conversion of alcohol back to acetaldehyde and enter back into the citric acid cycle. So, first they learned how to make an environmental poison to give them exclusive access to a food source, and then that same machinery was adapted to better allow them to eat that poison, permitting them recover some of the energy lost in secreting it.


*"Beer is proof that God loves us and wants us to be happy," Benjamin Franklin.


Thomson JM, Gaucher EA, Burgan MF, DeKee DW, Li T, Aris JP, Benner SA (2005) Resurrecting ancestral alcohol dehydrogenases from yeast. Nature Genetics 37:630-635.

Woolfit M, Wolfe K (2005) The gene duplication that greased society's wheels. Nature Genetics 37:566-567.

Categories

More like this

This is just unbelievable. At a day care center in Arkansas, 10 kids were accidentally given windshield wiper fluid instead of Kool-Aid: Child welfare investigators plan to talk to the owner of an Arkansas daycare center where 10 children were sickened after they were given windshield wiper fluid…
I saw this article in a couple of places before it dawned on me what the implication is: href="http://www.nytimes.com/2009/03/21/health/research/21alcohol.html">Drinkers' Red Face May Signal Cancer Risk By NICHOLAS BAKALAR Published: March 20, 2009 People whose faces turn red when they drink…
The previous entry on raspberry ketones got me thinking about supplements in general. For the most part they don't cause people problems - which is pretty remarkable, considering a lot of them do have real druglike molecules in them. Most people are taking these completely unsupervised, with only a…
Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein? I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of Parkinson's disease and I…

Not just beer, but also (genuflect when you say it)....MEAD!

SC is nutritious and tastes pretty good as a food yeast, too. I use it a lot as an ingredient to help mimic meat flavors in medium-advanced vegetarian cooking.

(You fanatical meat eaters can go ahead and deride me now for attempting to protect my breasts from the estrogen-dependent cancer my mother died from. Honestly, some people and their knee-jerk reactions whenever somebody says "vegetarian.")

By speedwell (not verified) on 26 Sep 2006 #permalink

Ooops, almost forgot. (genuflects in the general direction of mead)

By speedwell (not verified) on 26 Sep 2006 #permalink

I like "socially potent molecules."
Though ethanol's not my personal favorite one.

An interesting read. What caused the differences in top-fermenting and bottom-fermenting yeasts? Why do they exhibit such different behaviors?

By commissarjs (not verified) on 26 Sep 2006 #permalink

Ken siad:

Not just beer, but also (genuflect when you say it)....MEAD!

Speedwell said:

(genuflects in the general direction of mead)

As a brewer of said elixir, you may genuflect in my direction.

Which reminds me... I need to rack a couple of batches this week...

We need to appreciate beer more.

PZ -- perhaps I can enlist the aid of your fellow blogger, MarkCC, to explain to you that 100% means all of something!

I can't appreciate beer any more than I already do, although I'll start putting some serious effort into trying to break this law.

We may owe more to yeast than we currently acknowledge.

One of the biggest problems in studying human history is figuring out why we moved from being hunter-gatherers to agriculturalists, when all time-and-motion studies conclude that hunter-gatherers spend far less time working than farmers.

Some researchers have suggested that we became agriculturalists in order to cultivate and guarantee a steady supply of beer. All of the extra effort and tedium of farming was rewarded by beer. Farmers stayed in one place, created communities, used stored crops and quiet times of the year to create labour specialists, which created trade, then cities . . . and culminated in us!

And we all owe it to BEER, and the creator of beer . . YEAST!

Birds and wasps are known to experience but not necessarily to be put off by ingesting fruit-derived alcohol. Would fermentation act as a way to make fallen or imperfectly attractive fruits exceptionally desirable to browsing herbivores, or non-herbivores, for that matter, thereby increasing efficient dispersal of seeds? Are the sugar profiles of fruits sympathetic to fermentation, or have they evolved to be so?

Well, bigger critters seem to like the ethanol even better than the sugar, so I'd say the yeast's presence is providing some benefit. I'd be unsurprised to hear cases where the symbiosis has become near-obligatory.

By David Harmon (not verified) on 26 Sep 2006 #permalink

Zymurgosaurus dipsomanius?

I'd say my Latin is rusty, but mostly it was never there to begin with. So I'm unable to tell if this is a Latin joke, or I'm just not realizing how to pronounce that for maximum humor benefit.

Zymurgy - the study of fermentation
Saurus - greek for beast I think
Dypsomnia - the craving for alcohol

Zymurgosaurus Dipsomanus - The fermentation studying beast that craves alcohol.

Or something like that.

I've never found the taste of lactic acid to be "vinegary." Maybe you're thinking of acetic acid instead?

It may also be noted that our enzymes reverse the process, converting ethanol back into acetaldehyde, which is pretty toxic, but is rapidly converted to acetic acid by a dehydrogenase.

Mmmmmmm, Homebrew! I love the fact that its "alive", and the live yeast helps put the B vitamins back into your system. I really enjoy watching the yeast take off in my glass primary.

"To alcohol - the cause of, and the solution to, all life's problems" Homer Simpson

By ecostudent (not verified) on 26 Sep 2006 #permalink

Anyone know which organisms or pathways produce the methanol and fusel oils found in moonshine?

By Heterocronie (not verified) on 26 Sep 2006 #permalink

"they've been busily making alcohol that has gone undrunk by humankind for tens of millions of years"

Damn. I hate to see good booze wasted, don't you?

By Bloviator (not verified) on 26 Sep 2006 #permalink

Hal, many years ago there was an article in the back of the Smithsonian Magazine about animals and birds that liked to get drunk on natural sources of alcohol. I particularly remember reading about elephants looking for overripe marula fruit. However, Wikipedia distrusts the story of elephants getting tipsy on marula, so apparently there a pressing need for more research here.

Wikipedia distrusts the story of elephants getting tipsy on marula, so apparently there a pressing need for more research here.

I'm all for selfless science, but I've got enough problems keeping my own liquor cabinet stocked, thanks very much.

I ain't about to start sharing with elephants!

Them suckers is humongous! They drink lots! Getting my drift here? Some research is too expensive for society to support. Physics may be pushing the envelope (SCSC ring any bells?). But funding the budget for drunk elephants? Definitely beyond the envelope!

By Steviepinhead (not verified) on 26 Sep 2006 #permalink

I don't know about elephants, but I watched a flock of cedar waxwings eating mountain ash berries that had been on the tree all winter and they were falling out of the tree after a while. I have also watched black bears drink beer, and remember reading a story from out in the northwest where a bear raided a campsite and drank all their Ranier beer while leaving all but one of another brand. Sounds like a good ad campaign.

By ecostudent (not verified) on 26 Sep 2006 #permalink

Rainier. Just saying.

But, yeah, those bears have pretty discriminating taste buds.

Yar, yar!

By Steviepinhead (not verified) on 26 Sep 2006 #permalink

Malt does more than Milton can

To justify God's ways to man.

Heh, Steviepinhead--don't know how long you've been in Seattle, but you may or may not remember a sketch comedy series on KING 5 called "Almost Funny^H^H^H^H^HLive".

As John Keister put it, the Japanese beer executives were visiting the Rainier plant to learn how much lighter fluid to put in the beer.

Just sayin'...

Bit of a side topic, but I like the title of that reference: "The gene duplication that greased society's wheels." Might have been even better as, "The evolutionary twist that proves God loves us."

Can anyone point me to any on-line collections of catchy paper titles (real ones, that is)?

"Hal, many years ago there was an article in the back of the Smithsonian Magazine about animals and birds that liked to get drunk on natural sources of alcohol. I particularly remember reading about elephants looking for overripe marula fruit. However, Wikipedia distrusts the story of elephants getting tipsy on marula, so apparently there a pressing need for more research here."
I'm sure I've seen video footage of animals eating overripe fallen fruit and apparently getting drunk off it...

One Autumn in Alabama, my mother was running around the yard grabbing cats and taking them inside, to protect the drunken robins staggering around (I think it was chinaberries).

They don't do it by making lactic acid, though (thank goodness--if they did, fermentation would produce a vinegary acid).

Well, some organisms do, and those organisms are themselves very valued as part of the fermentation process. Can't enjoy a good pickle without lactobacillus. And, heck, you couldn't have a good lambic beer without the contribution of our friend brettanomyces, which produces acetic acid.

So, a related question. Why is it that female humans have less efficient ethanol metabolism than males (on average) even controlling for body mass?

Women don't necessarily have less efficient ethanol metabolisms, it's just that men tend to be better at functioning with fewer functioning brain cells.

By david rickel (not verified) on 27 Oct 2006 #permalink

Saurus - greek for beast I think

"Lizard". Traditionally used in dinosaur names because Sir Richard Owen in 1842 thought dinosaurs actually were lizards.

Women don't necessarily have less efficient ethanol metabolisms, it's just that men tend to be better at functioning with fewer functioning brain cells.

I wanted to write that men are probably more often used to alcohol, but that's probably the same...

By David Marjanović (not verified) on 28 Feb 2007 #permalink

Is it known what mutation(s) will reverse the reaction?

By Billy Sands (not verified) on 01 Jan 2008 #permalink

No methanol in fusel oil, PTL. Speedwell, I probably would help you protect your breasts. Alcohol brings that behavior out in me. Do lunch? I'm a vegi too.

By BlindSquirrel (not verified) on 23 Feb 2008 #permalink

Saurus - greek for beast I think

"Lizard". Traditionally used in dinosaur names because Sir Richard Owen in 1842 thought dinosaurs actually were lizards.

Women don't necessarily have less efficient ethanol metabolisms, it's just that men tend to be better at functioning with fewer functioning brain cells.

I wanted to write that men are probably more often used to alcohol, but that's probably the same...

By David Marjanović (not verified) on 28 Feb 2007 #permalink

"They then took modern yeast, removed their Adh1 and Adh2 genes, and replaced them with AdhA. Voilà, they have yeast from the Age of the Dinosaurs."

Why would they put AdhA in another yeast cell? It already makes alcohol. What they need to do is take the AdhA gene and replace the lactic acid gene in my muscles. That way when I go running I don't get lactic acid buildup, but instead get drunk! Americans would struggle with their weight so much less if they could get drunk for free while burning calories, instead of taking in calories.

About those animals eating overripe fruit. I also once saw a video about drunken baboons. The next morning there was one with a hangover. Extremely hilarious was the fact that he took the posture of The Thinker by Rodin...

Did yeast evolve this enzyme to make a byproduct to inhibit its competitors, or did it evolve it to eat this byproduct?

Am I missing something? Because that question doesn't make much sense to me. How could it have evolved that enzyme to consume alcohol before it became able to produce alcohol? Where would the alcohol to be consumed have come from?

If birds were staggering from eating china berries, I don't think it was because of alcohol. I think china berries are toxic. Wasn't there a bit in Jurassic Park where stegosauruses were sick from eating china berries?

By gaypaganunitar… (not verified) on 28 Nov 2008 #permalink