Pharyngula

α-actinin evolution in humans

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Perhaps your idea of the traditional holiday week involves lounging about with a full belly watching football — not me, though. I think if I did, I’d be eyeing those muscular fellows with thoughts of muscle biopsies and analyses of the frequency of α-actinin variants in their population vs. the population of national recliner inhabitants. I’m sure there’s an interesting story there.

In case you’re wondering what α-actinin is, it’s a cytoskeletal protein that’s important in anchoring and coordinating the thin filaments of actin that criss-cross throughout your cells. It’s very important in muscle, where it’s localized in the Z-disk at the boundaries of sarcomeres, the repeated contractile units of the muscle. This diagram might help you visualize it:

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Actin (green), myosin (red). Rod-like tropomyosin molecules (black lines). Thin filaments in muscle sarcomeres are anchored at the Z-disk by the cross-linking protein α-actinin (gold) and are capped by CapZ (pink squares). The thin-filament pointed ends terminate within the A band, are capped by tropomodulin (bright red). Myosin-binding-protein C (MyBP-C; yellow transverse lines).

The most prominent elements in the picture are the thin filaments (made of actin) and thick filaments (made of myosin) which slide past each other, driven by motor proteins, to cause contraction and relaxation of the muscle. The α-actinin proteins are the subtle orange lines in the Z disks on the left and right.

The α-actinin proteins are evolutionarily interesting. In vertebrates, there are usually four different kinds: α-actinin 1, 2, 3, and 4. 1 and 4 are ubiquitous in all cells, since all cells have a cytoskeleton, and the α-actinins are important in anchoring the cytoskeleton. α-actinin-2 and -3 are the ones of interest here, because they are specifically muscle actinins. α-actinin-2 is found in all skeletal muscle fibers, cardiac muscle, and also in the brain (no, not muscle in the brain, there isn’t any: in the cytoskeleton of neurons). Just to complicate matters a bit, α-actinin-2 is also differently spliced in different tissues, producing a couple of isoforms from a single gene. α-actinin-3 is not found in the brain or heart, but only in skeletal muscle and specifically in type II fast glycolytic muscle fibers.

Muscle fibers are specialized. Some are small diameter, well vascularized, relatively slow fibers that are optimized for endurance; they can keep contracting over and over again for long periods of time. These are the fibers that make up the dark meat in your Christmas turkey or duck. Other fibers are large diameter, operate effectively anaerobically, and are optimized for generating lots of force rapidly, but they tend to fatigue quickly — and there are more of these in the white meat of your Christmas bird. (There are also intermediate fiber types that we won’t consider here.) Just keep these straight in your head to follow along: the fast type II muscle fibers are the ones that you use to generate explosive bursts of force, and may be enriched in α-actinin-3; the slower fibers are the ones you use to keep going when you run marathons, and contain α-actinin-2. (There are other even more important differences between fast and slow fibers, especially in myosin variants, so differences in α-actinins are not major determinants of muscle type.)

Wait, what about evolution? It turns out that invertebrates only have one kind of α-actinin, and vertebrates made their suite of four in the process of a pair of whole genome duplications. We made α-actinin-2 and -3 in a duplication event roughly 250-300 million years ago, at which time they would have been simple duplicates of each other, but they have diverged since then, producing subtle (and not entirely understood) functional differences from one another, in addition to acquiring different sites of expression. α-actinin-2 and -3 in humans are now about 80% identical in amino acid sequence. What has happened in these two genes is consistent with what we know about patterns of duplication and divergence.

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Using sarcomeric α-actinin as an example, after duplication of a gene capable of multiple interactions/functions, there are two possible distinct scenarios besides gene loss. A: Sub-functionalisation, where one interaction site is optimised in each of the copies. B: Neo-functionalisation, where one copy retains the ancestral inter- action sites while the other is free to evolve new interaction sites.

So what we’re seeing in the vertebrate lineage is a conserved pattern of specialization of α-actinin-3 to work with fast muscle fibers — it’s a factor in enhancing performance in the specific task of generating force. The α-actinin-3 gene is an example of a duplicated gene becoming increasingly specialized for a particular role, with both changes in the amino acid sequence that promoted a more specialized activity, and changes in the regulatory region of the gene so that it was only switched on in appropriate muscle fibers.

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Duplication and divergence model proposed by this paper. Before duplication the ancestral sarcomeric α-actinin had the functions of both ACTN2 and ACTN3 in terms of tissue expression and functional isoforms. After duplication, ACTN2 has conserved most of the functions of the preduplicated gene, while ACTN3 has lost many of these functions, which may have allowed it to optimise function in fast fibres.

That’s cool, but what we need is an experiment: we need to knock out the gene and see what happens. Mutations in α-actinin-2 are bad—they cause a cardiomyopathy. Losing α-actinin-4 leads to serious kidney defects (that gene is expressed in kidney tissue). What happens if we lose α-actinin-3?

It turns out you may be a guinea pig in that great experiment. Humans acquired a mutation in the α-actinin-3 gene, called R577X, approximately 40-60,000 years ago, and this mutation is incredibly common: about 50% of individuals of European and Asian descent carry it, and about 10% of individuals from African populations. Furthermore, an analysis of the flanking DNA shows relatively little recombination or polymorphism — which implies that the allele has reached this high frequency relatively recently and rapidly, which in turn implies that there has been positive selection for a nonsense mutation that destroys α-actinin-3 in us. The data suggests that a selective sweep for this variant began in Asia about 33,000 years ago, and in Europe about 15,000 years ago.

There is no disease associated with the loss of α-actinin-3. It seems that α-actinin-2 steps up to the plate and fills the role in type II fast muscle fibers, so everything functions just fine. Except…well, there is an interesting statistical effect.

The presence of a functional α-actinin-3 gene is correlated with athletic performance. A study of the frequency of the R577X mutation in athletes and controls found that there is a significant reduction in the frequency of the mutation among sprinters and power-lifters. At the Olympic level, none of the sprinters in the sample (32 individuals) carried the α-actinin-3 deficiency. Among Olympic power lifters, all had at least one functional copy of α-actinin-3.

Awesome. Now I’m wondering about my α-actinin-3 genotype, and whether I have a good biological excuse for why I always got picked last for team sports in high school gym class. This is also why I’m interested in taking biopsies of football players…both for satisfying a scientific curiosity, and for revenge.

You may be wondering at this point about something: α-actinin-3 has a clear beneficial effect in enhancing athletic performance, and its conservation in other animal species suggests that it’s almost certainly a good and useful protein. So why has there been positive selection (probably) for a knock-out mutation in the human lineage?

There is a weak correlation in that study of athletic performance that high-ranking athletes in endurance sports have an increased frequency of the R577X genotype; it was only seen in female long-distance runners, though. More persuasive is the observation that α-actinin-3 knockouts in mice also produced a shift in metabolic enzyme markers that are indicative of increased endurance capacity. The positive advantage of losing α-actinin-3 may be more efficient aerobic metabolism in muscles, at the expense of sacrificing some strength at the high end of athletic performance.

This is yet another example of human evolution in progress—we’re seeing a shift in human muscle function over the course of a few tens of thousands of years.


Lek M, Quinlan KG, North KN (2009) The evolution of skeletal muscle performance: gene duplication and divergence of human sarcomeric alpha-actinins. Bioessays 32(1):17-25. [Epub ahead of print]

MacArthur DG, Seto JT, Raftery JM, Quinlan KG, Huttley GA, Hook JW, Lemckert FA, Kee AJ, Edwards MR, Berman Y, Hardeman EC, Gunning PW, Easteal S, Yang N, North KN (2007) Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans. Nat Genet.39(10):1261-5.

Yang N, MacArthur DG, Gulbin JP, Hahn AG, Beggs AH, Easteal S, North K (2003) ACTN3 genotype is associated with human elite athletic performance. Am J Hum Genet 73(3):627-31.

Comments

  1. #1 cervantes
    December 23, 2009

    A very intelligently designed essay, I must say.

  2. #2 Glen Davidson
    December 23, 2009

    This is the kind of stuff that convinces me that creationists are complete believers in accident. We have reasons for why things are as they are (sometimes even “accident,” but entirely explicable), and all they ever have is accident.

    But it’s accident in the mind of God, so it’s all good.

    Glen D
    http://tinyurl.com/mxaa3p

  3. #3 HenryS
    December 23, 2009

    Very interesting…the 60,000 years time frame is about the time that it is thought that a very small number of modern humans successfully exited East Africa and populated the rest of the world.

    It would be interesting to compare muscle/genetics of East and West African world class runners. People of West African heritage have dominated “sprint” for decades and now distance runners of East African heritage are now dominating distance running. The “good” muscle genes may have stayed in Africa.

  4. #4 Sven DiMilo
    December 23, 2009

    That’s very interesting. I wonder about the still-missing mechanistic details–how does ?-actinin-3 enhance anaerobic sprinting performance, and how might losing ?-actinin-3 increase aerobic endurance? Seems like it must be more than a simple anchor to the Z-disc.

    One quibble: myosin isthe motor protein.

  5. #5 madbull
    December 23, 2009

    does this mean that humans no longer need that kind of muscle power so there is positive selection to cut down on the energy requirements of maintaining such power ?
    I am just asking, cos as interested as I am in evolution, biology isn’t one of my strong points

  6. #6 oihorse
    December 23, 2009

    Awesome essay. I love reading well-written science where complicated topics get boiled down without being dumbed down.

    Thanks PZ!

  7. #7 nastasie
    December 23, 2009

    I just wanted to express how fascinating I found this study as well as your explanation. First of all, because I was able to follow, and second, well, it’s an engaging narrative, I guess. It reads like a well plotted story, which I just realised is the feeling I always get when I’m hearing about how a certain research was carried out. Makes me want to look for a, erm, sequel.

  8. #8 MadScientist
    December 23, 2009
  9. #9 Margaret
    December 23, 2009

    The data suggests that a selective sweep for this variant began in Asia about 33,000 years ago, and in Europe about 15,000 years ago.

    That’s too long ago to be correlated with the development of agriculture, though endurance rather than sprinting capability would certainly be used in agriculture.

    Could somebody who knows something about early human lifestyles speculate on why this might be useful?

  10. #10 Carax
    December 23, 2009

    Considering the subject of elite human physical performance, the less deficient one is in -actinin-3, the longer the endurance in running ability which explains why an advantageous genetic profile probably helps win 26 mile marathons.

    Love this stuff even though I don’t understand it all.

  11. #11 LKL
    December 23, 2009

    That was fun to read; I’m going to send it out on my email list. Thanks for taking the time to write that, PZ.

  12. #12 Knockgoats
    December 23, 2009

    Margaret@9,
    Domestication of the dog, with a consequent shift from ambush hunting to long-distance pursuit? Recent finds push domestication back to over 30,000 years ago in western Asia.

  13. #13 Peter Ashby
    December 23, 2009

    Well one use of endurance is if your hunting technique involves running game to exhaustion. The Saan Bushmen of the Kalahari desert in SW Africa employ or did employ this technique. It is useful if you don’t have weapons that can kill efficiently from a distance so you need to get close to prey that are often dangerous with hoof and horn/antler.

    Then there is the idea of having to travel far to get animals for food, then of course you need to trek back to camp with the spoils of your successful hunt or to do it the next day and the next until you are successful. The sprinters get left behind pretty quickly in that scenario and since we know that success in hunting equals success in the mating game for male hunter gatherers this gives a mechanism for spread.

    We are perhaps too used to the idea of early modern man driving mammoths off cliffs or bringing down prey with a single spear throw or much more modern hunter gatherers with atlatls, recurved or long bows, horses etc to remember what it must have been like to hunt with much less efficient tools in tundra environments during the ice ages when we know humans were successfully living in such environments in what is now Southern Russia. There would have been prey there, just not many and not on their doorstep.

  14. #14 Noni Mausa
    December 23, 2009

    “…and also in the brain (no, not muscle in the brain, there isn’t any…)”

    I could name a few candidates for muscle-in-the-brain…

    Bone, too.

    Noni

  15. #15 Margaret
    December 23, 2009

    Thanks Knockgoats! I hadn’t thought that different styles of hunting would require different types of muscle strength. Does the evidence of more ancient domestication of dogs include any indications of their use for hunting or just their presence around human garbage dumps? Hmmm. I don’t even know how you’d tell that. Evidence of a change in which game animals are caught?

  16. #16 Margaret
    December 23, 2009

    Well one use of endurance is if your hunting technique involves running game to exhaustion. The Saan Bushmen of the Kalahari desert in SW Africa employ or did employ this technique.

    It sounds like it would be interesting to test the Saan for this muscle mutation.

    …you need to trek back to camp with the spoils of your successful hunt…

    Does the timing of the spread of the mutation correlate at all with the establishment of human camps (to return to) instead of everybody tramping after the game? Or with game being larger and farther away from camp? Or with human spread to less friendly climates where camp (with shelters) must be established to survive?

  17. #17 Knockgoats
    December 23, 2009

    Margaret@15,
    Not AFAIK. According to this, the case I was thinking of is the skull of a “wolf in transition to a dog”, dated to 31,700BP, and the main change, the shortening of the muzzle, could be due just to a change in diet, perhaps linked to the beginning of human-dog association – so, maybe just hanging around garbage dumps! There’s a bit in Dawkins’ latest about speculation that the first stage of domestication was initiated by wolves in this way. I admit, I rather like the idea of domestication being kind of mutual in the case of human and dog – and cat, presumably – it must have been cats’ idea to start hanging around grain stores.

  18. #18 Insightful Ape
    December 23, 2009

    You don’t need a muscle biopsy to check for mutations. A simple blood test will do.
    Sorry PZ, you are not getting your revenge.

  19. #19 hje
    December 23, 2009

    Excellent post on an interesting protein (especially so, since I have milligrams of bovine cardiac alpha-actinin socked away in the minus 80).

  20. #20 PZ Myers
    December 23, 2009

    I know. The papers have methods sections. But you know, taking a big needle to football players sounds like so much fun…

  21. #21 Margaret
    December 23, 2009

    Knockgoats@17
    Thanks for the link.

    Maybe the muscle change is linked to trekking back and forth to camp as suggested by Peter Ashby@13 and the domestication of the dog is linked to wolves hanging around the resulting garbage dumps near the camps. It sounds like the actual use of dogs came later.

    Fun speculation.

  22. #22 chuckgoecke
    December 23, 2009

    Sounds like humans have been self selecting themselves to have less white meat. Humm…maybe we’re not the other white meat.

  23. #23 Antiochus Epiphanes
    December 23, 2009

    “But evolution can’t create new information!”

    (fingers in ears) “Jingle Bells! Jingle Bells! Jingle all the waaaaaaaayyy!”

  24. #24 sasqwatch
    December 23, 2009

    If it helps any, the outlook for footballers ain’t all that rosy. If any of you have/are footballers, even at the high school level, may I suggest stage band or chess club?

    Thanks much for the trip through memory lane. Before my stint in sex research (not the “hard” science kind), my training was in Biochem. Makes me nostalgic.

  25. #25 erich.oliphant
    December 23, 2009

    Wow, with all the cracker-stabbing and what have you, it’s easy to forget that PZ is a power nerd, lol.

    But seriously, great post. Very interesting. But it all seems so ‘irreducibly complex’ ROFL

  26. #26 Newfie
    December 23, 2009

    but you won the ‘trophy’. :)

  27. #27 bungoton
    December 23, 2009

    Hey sasquatch,
    I was on my high school football team and in the chess club. It is possible to be a nerd and an athlete without giving up too much on either side.

    Ummm, I forget what I was going to say next, I’m sure it was very clever.

  28. #28 mokele
    December 23, 2009

    Their molecular clock is wrong – alpha-actinin 2 & 3 cannot have split 300 mya.

    Ten seconds on google shows that zebrafish have it, and the paper itself focuses on the gene duplication events at the origins of Craniata and Gnathostomata, which pushes the date back to 462 mya.

  29. #29 drdale
    December 23, 2009

    @ #4, Cell biologists consider the motor proteins to be kinesin and dynein which are plus- and minus- end directed. In which the proteins use ATP to “walk” along microtubules.

  30. #30 F
    December 23, 2009

    Wicked. That piece is a lot more accessible to me than a lot of the other stuff I read (or attempt to read).

  31. #31 destlund
    December 23, 2009

    Well one use of endurance is if your hunting technique involves running game to exhaustion. The Saan Bushmen of the Kalahari desert in SW Africa employ or did employ this technique. It is useful if you don’t have weapons that can kill efficiently from a distance so you need to get close to prey that are often dangerous with hoof and horn/antler.

    I would be careful with that one: PZ pointed out some enhancement to aerobic respiration, and whether you’re using fast twitch muscle fibers or not, you’re going to make use of anaerobic respiration after a short time. It sounds more like the endurance boost would be helpful to nomads trekking through stretches of desert or tundra, feeding on scarce food resources.

  32. #32 mdcaton
    December 24, 2009

    This is an excellent article. I’m a distance runner and I’m tired of arguing with sprinters and lifters about how they’re supposedly healthier and they’re somehow more true to humans’ evolutionary heritage. More like they’re throwbacks. Hey guys, once we left Africa and had FoxP2 and better tools and organization it was all about chasing game over the Eurasian steppes for miles and miles! You dummies! These are the same morons who avoid carbs like the plague and stick to what is supposedly a paleolithic diet (vegetables and lean meats only). And whaddya know, just recently there was an article showing that 100,000 years ago, people were eating lots of grains! It’s bad times for the high-impact paleo folks all-around!

    In closing, weight-lifters and sprinters are apostates and must be excommunicated from the CoE (Church of Exercise) for their heresy. Schism! Schism!

  33. #33 destlund
    December 24, 2009

    More like they’re throwbacks.

    Much as I’d agree with you on most of your post, that part made me cringe. It’s both incorrect and inappropriate. On the diet tip, I’d guess that early man ate mostly seeds, nuts, fruits, and meats, possibly sprinkled with herbs and grasses. What we think of as vegetables are mostly the products of artificial selection, as are what we think of as grains. Predecessors of wheat/corn/barley/etc. probably didn’t provide a lot by way of carbs.

  34. #34 destlund
    December 24, 2009

    It’s very late and my posts aren’t SIWOTI inducing denial/flame/hate/crazy, but I’m really interested in this, and I can’t back up my statements with peer-reviewed literature. I’d like to see someone respond in either the affirmative or negative.

  35. #35 Rorschach
    December 24, 2009

    I’m currently reading “Endless forms most beautiful” where Carroll also talks about the role of duplication events for specialization, he gives the example of middle ages people using knifes not only to cut meat but to spear it and put in their mouth, and how from this duplication event came the “evolution” of the fork, its amazing stuff.

    I can only recommend that book to anyone interested in a brushup of their biology knowledge, I’m immensely enjoying it.

  36. #36 Sven DiMilo
    December 24, 2009

    Cell biologists consider the motor proteins to be kinesin and dynein

    Cell biologists also know that the motor protein relevant to muscle (because it exerts force on actin microfilaments instead of tubulin microtubules) is myosin.

  37. #37 Sven DiMilo
    December 24, 2009

    mdcaton:
    show ‘em this

  38. #38 Sven DiMilo
    December 24, 2009

    PZ pointed out some enhancement to aerobic respiration, and whether you’re using fast twitch muscle fibers or not, you’re going to make use of anaerobic respiration after a short time.

    Not sure what your point is here. Enhanced aerobic support of exercise should improve endurance whether you’re running or trekking.

  39. #39 Sven DiMilo
    December 24, 2009

    I’d guess that early man ate mostly seeds, nuts, fruits, and meats, possibly sprinkled with herbs and grasses.

    Also tubers, eggs, bacon, and beer.

  40. #40 destlund
    December 24, 2009

    Not sure what your point is here. Enhanced aerobic support of exercise should improve endurance whether you’re running or trekking.

    Not when you deplete your oxygen supply through extended strain. Running long distances, whether marathon or sprint style, will at some point switch the body over to anaerobic respiration. I believe that point is called “hitting the wall.” Enhancements to aerobic respiration will do no good there. Walking long distances does not cause the body to go into oxygen debt, so enhancements to aerobic and not anaerobic respiration will do more good there.

  41. #41 destlund
    December 24, 2009

    Also tubers, eggs, bacon, and beer.

    How could I forget?! No man could survive without bacon and beer!

  42. #42 Sven DiMilo
    December 24, 2009

    Not when you deplete your oxygen supply through extended strain. Running long distances, whether marathon or sprint style, will at some point switch the body over to anaerobic respiration. I believe that point is called “hitting the wall.”

    You are mistaken. “Oxygen debt” is a metaphor. Oxygen supplies, (the amount and arterial saturation of hemoglobin) do not decline during aerobic exercise. The phenomenon of “hitting the wall” is believed to represent some combination of glycogen depletion (i.e. carbohydrate fuel supplies) and other types of fatigue.
    Aerobic exercise endurance is limited mostly by delivery constraints; the oxygen supply is set by the maximum cardiovascular performance (basically cardiac output).
    It is therefore correct that pretty much all exercise of at least moderate intensity involves some anaerobic component, but most of this occurs right at the beginning of the exercise bout (because the cellular aerobic machinery takes time to get cranked up)(also a metaphor) and during occasional bouts of increased speed, hill-climbing, etc., that the heart can’t keep up with.
    Sprinting is different; any full-out effort lasting less than a few minutes is almost all anaerobic from the get-go. Hence the much faster fatigue, of muscular origin.

    (gah, siwoti…I got stuff to do)

  43. #43 destlund
    December 24, 2009

    Sven DiMilo,
    Cool. Thanks.

  44. #44 destlund
    December 24, 2009

    This could be resolved with science. PZ mentioned Olympic sprinters and power lifters. If the endurance advantage associated with the mutation assists with long-distance running, then we should see the reverse trend among Olympic marathon runners.
    I’m still betting that the selection had more to do with crossing geographical barriers than with some advance in civilization leaving Africa in the dust. The latter doesn’t pass the “racial inferiority” sniff test.

  45. #45 Jim
    December 26, 2009

    Your science is sufficiently advanced. It is indistinguishable from magic.

    Best wishes for the season and the new year, from a knuckle-dragging believer.

  46. #46 Dania
    December 26, 2009

    Your science is sufficiently advanced. It is indistinguishable from magic.

    You’re right, Jim. Why all those big sciency words when you can explain everything in a simple, not-like-magic manner such as:

    And God said, Let there be light: and there was light.

  47. #47 Jim
    December 27, 2009

    Dania said:

    You’re right, Jim. Why all those big
    sciency words when you can explain
    everything in a simple, not-like-magic
    manner such as:

    And God said, Let there be light: and
    there was light.

    Because I don’t think that explains everything. (I won’t annoy you with what I think it does explain.)

    I was actually trying to make a joke about the difficulty I have following an excellent, clear explanation of a subject about which I know slightly less than the cube root of nothing.

    It wasn’t a very good joke, I admit, but Cervantes @#1 had already used:

    A very intelligently designed essay, I must
    say.

  48. #48 Rorschach
    December 27, 2009

    Why all those big sciency words when you can explain everything in a simple, not-like-magic manner such as:

    And God said, Let there be light: and there was light.

    Or this one :

    “In the beginning, god created the heaven and the earth–doesnt go into detail…just trust me, I did”

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