As we are so often reminded by proponents of Intelligent Design creationism, we contain molecular "machines" and "motors". They don't really explain how these motors came to be other than to foist the problem off on some invisible unspecified Designer, which is a poor way to do science—it's more of a way to make excuses to not do science.
Evolution, on the other hand, provides a useful framework for trying to address the problem of the origin of molecular motors. We have a theory—common descent—that makes specific predictions—that there will be a nested hierarchy of differences between motors in different species. Phylogenetic analysis of variations between species allows us to reconstruct the history of a molecule with far more specificity than "Sometime between 6,000 and 4 billion years ago, a god or aliens (or aliens created by a god) conjured this molecule into existence by unknown and unknowable means".
Richards and Cavalier-Smith (2005) have applied tested biological techniques to a specific motor molecule, myosin, and have used that information to assemble a picture of the phylogenetic history of eukaryotes.
Myosin should be a familiar protein to all of us: it's an important component of muscle, and is the motor that drives muscle contractions. Like most biological machines, its function can actually be reduced to something fairly simple, and the complexity arises from the multitude of permutations, the many little tweaks that have been made to it, in a long, long history of random changes filtered by selection.
Myosin is a ratchet. It has a globular head that has enzymatic activity: it hydrolyzes a molecule used for energy storage, ATP. When it burns the energy released from the breakdown of ATP, it undergoes a conformation change, bending the head relative to the tail. It's a small thing, really, a tiny shift in the shape of the molecule.
A small thing repeated many, many times by a large number of molecules can add up to a fair amount of force, however. These small shifts in shape are coupled into a contraction cycle in the muscle. The myosin burns ATP to ADP to change shape, it binds to another molecule, it releases the spent ADP, it flexes back, shifting the other molecule; then it burns more ATP, binds again to the molecule, flexes, and releases. Burn, bind, flex, release…over and over again, shifting sliding strands of protein a tiny fraction of a millimeter at a time. That's the engine that drives every contraction of your muscles.
You have 12 different forms of the myosin gene. Why the diversity? Because they have slightly different properties: what they bind to best, how fast they change shape, when and where they are expressed. There's a special myosin for your heart muscle, a different one for slow muscles for endurance, another for fast twitch muscles that generate lots of power quickly. There's a smooth muscle myosin and a fetal myosin.
Myosin is present in other organisms, too, not just animals with muscles, so don't think of it as simply a muscle component. Amoebae, plants, and mushrooms also have essential myosins. Myosin is a general purpose ratchet that shifts proteins, especially cytoskeletal proteins, relative to one another. Our cells use it to transport organelles and proteins from one part of the cell to another, and we wouldn't be able to sustain long nerves without myosin to move essential components from the cell body to the periphery. Amoebae use it to push out pseudopods; amoeboid movement depends on it. They drive cytokinesis, the process of cell division. If you're a eukaryote, it doesn't matter whether you are capable of pumping iron or not—you've got myosin or a member of the related kinesin gene family to power physical movements within cells.
All of these diverse functions in diverse organisms use the same recognizable core module to do their job, that ATP-binding globular head, but they vary in activity and binding properties to other molecules and in that associated tail you can see in the cartoons above. That means one can fish within genomic data and find the recognizable part of the myosin, and also catalog the differences and assemble a picture of the molecule's evolutionary history. Richards and Cavalier-Smith identified 37 different types of myosin in their investigation, used characters from each to put together a table of similarities and differences.
For instance, plants have a feature in their myosin called the TH1-FYVE-like insert, which is not present in any animals, fungi, or amoebozoa, which suggests that this element evolved after the plant and animal lineages diverged. Likewise, animals and fungi share a MYTH4/FERM duplication that isn't present in any of the other groups, linking them together and almost certainly evolving well after the plant-animal separation. Putting all the information together yields a eukaryotic family tree.
Schematic tree showing myosin-derived synapomorphies (green bars) and three previously published shared characters (grey bars). Yellow bars indicate synapomorphy plus secondary loss. MYSc, myosin head domain.
This tree corresponds well with similar trees generated from other kinds of data; it doesn't place fungi closer to plants than animals, for instance, despite the fact that you might superficially think mushrooms and trees have more in common than mushrooms and monkeys. This is another strength of the scientific approach: we get answers that are consistent with one another and with the idea of relationships by descent.
They were also able to infer some of the properties of the last common ancestor of all eukaryotes. It had three kinds of myosin, that differ mainly in the structure of the tail.
Richards and Cavalier-Smith propose that there were three ancestral myosins in the earliest eukaryotes, each with distinct tail domain structures. Listed are examples of organisms or cells expressing members of each myosin group and their known functions. The TH1 domain would probably bind to charged lipids and target these myosins to membranes. The SMC domain would promote dimer formation and the DIL and MyTH4/FERM domains would target myosins to their cargo or subcellular location.
In addition to three myosin types, it would have also had a single cilium, mitochondria, and pseudopodia, and would probably have been a motile cell. This is one of the powers of modern evolutionary biology: although we weren't there, and although we don't even have fossils of these organisms, the chain of evidence and logical inference can give us a fuzzy glimpse of a creature that lived over 2 billion years ago.
Richards TA, Cavalier-Smith T (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature 436(7054):1113-1118.
Titus MA (2005) A treasure trove of motors. Nature 436(7054):1097-1099.
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I probably wouldn't have used the term "motor" in this discussion, even though it is commonly used in the literature when discussing these things. The IDiots will jump all over this, quote mine it, etc. You're a good guy and I wouldn't want you inadvertently helping the evil enemy. BTW, great post. I got the rudiments of myosin, actin, etc in medical school but forgot most of it. It is always nice to have a refresher course and expand my knowledge beyond just the medical realm when discussing these things.
Ah, so this explains the "fast twitch, slow twitch" stuff we were told about when running track...
What's so bad about "motor"?
It IS a motor: it converts chemical potential energy to mechanical kinetic energy.
Hypothesis:
Under ID theory, the different myosins, whihc are optimcal for different purposes, will have a perfect match with demand for those functions.
One criterion for rejection of this hypothesis: Under alternative theories, such as evolution, there could be such a matching up of form and function, but there should be quirks ... the ideal myosin for a certain function on one part of the phylogenetic tree would be unavailable due to phylogenetic constraints. In such a case, the locally used myosin would be one adapted from another (ancestral) form.
Honestly, I do not know the answer to this question in advance. My ignorance in this case therefore makes this a "real" hypothesis.
Hypothesis:
Movement is one of the most demanding systems in any "higher" orgnaism. The total energy that goes through an individual over a lifetime that is spent on movement of tissue of one form or another (relative to other functions) is very high, and this is critically important. Therefore, the energy supply should be optimized or adaptive in most ways.
Under ID Theory, the energy sources that are used, while presumably limited to "available natural" sources, for movement of tissues (such as locomotion, or moving the blood supply around, etc.) should be diverse. There are many alternative sources of energy, for both storage and use.
Under ID theory, good design calls for Myosin a) in any given setting to use multiple sources of energy (i.e., glucose and other sugars) in action, and b) to use different kinds of energy depending on the typical demands of a given species (i.e., we would expect aquatic vs. terrestrial forms, endo- vs ecto-thermic forms, etc. etc. to use different kinds of energy to make movement happen.
Well, I do know the answer to this question in advance ... and it does not look too good for the ID hypothesis....
"It IS a motor: it converts chemical potential energy to mechanical kinetic energy."
Yea, I agree, "motor" is good, let's keep "motor."
Professo Myers, do you have any updates on the prokaryote-eukaryote transition itself? That seems to be quite difficult to account for, even Dawkins says it is no less of a mystery than the initiation of life itself. Particularly vexing is that the DNA synthesis and translation are biochemically different.
There recently was a very good Nature paper on the latest hypothesis: the mitochondria introduced introns, which were originally transposons or something, and the only way to survive that was the evolution of the nucleus. It's explained in quite some detail. I just can't find the paper right now...
mndarwinist, why do you say that DNA synthesis and translation are biochemically different? Most of the reaction steps are identical between bacteria and humans. And the endosymbiosis theory of the origin of eukaryotes has been strongly supported by genome sequences and phylogenetic trees that show that mitochondria are related to a specific group of bacteria (Rickettsia, within the alpha-Proteobacteria).
Aren't archaea seen as a possible way for the prokaryote/eukaryote transition? Don't they share features of both kingdoms?
I have to admit that my cell biology is not up to date. The steps of transcription and translation, and of course the genetic codes are the same, but enzymes are not; and specifically, the Initiation and Elongation factors are different. Also removal of certain parts of mRNA before translation seems to be quite a radical step; as far as I am aware there are no transitional forms there(they must have existed at some point).
Namesake:
.. ,--Bacteria
.. |
---|
.. | .. ,--Archaea
.. | .. |
.. `----|
....... |
....... `--Eukaryota
Tree-thinking.
(Ignore the dots; they are supposed to be whitespace. Time runs left to right.)
F***! Why does the preview use a different font than the actual article! Screwed up the careful spacing. Well, fortunately not much.
This is what you call one of those high-falutin' "rhetorical" questions, isn't it? Let's see... any prokaryotes here, raise your hands! Err, wait, I mean, extend your pseudopods! Or whatever you have....
Bueller? Bueller?
"Ah, so this explains the "fast twitch, slow twitch" stuff we were told about when running track..."
Yeah, I was always amazed in high school phys.ed. about the lack of information they gave that might have made it a little interesting. The weightlifting coach here at Caltech doesn't seem to do that, thankfully...she'll answer the questions or tell you what to look for, not just issue clouds of bullshit until you stop asking biological questions.
And I don't see any targets for quote-mining in this one. See, this is the sort of Pharyngula mol-bio post I really appreciate: it's not that mol-bio is too difficult for me, rather usually just that I find it uninteresting, but stirring in a good helping of phylogeny makes it awesome.
Being a total non-scientist, I skipped some of the more technical stuff, but this explanation of a basic process which we all take for granted is really fascinating.
Great post.
mndarwinist,
i'm always suspicious of people who pose such faux naive-sounding questions that they clearly consider stumpers. my advice is to always check out the PubMed database. I think that a large percentage of 1325 papers (including 156 reviews) when I searched "mrna splicing evolution" will contain thoughts on your question about plausible origins for introns and the various types of mRNA processing. I know the technical literature can be daunting, but you seem to be pretty up on things!
you may want to fact check the assertion about intiation/elongation factors. many (though of course not all) components of these complexes are highly conserved across all living things.
PZ, the text in the image 'musclemyosin.jpg' has been ruined by jpegization -- even if I blow it up until it fills the screen it's completely unreadable.
Nuthin' personal, but screw that.
Or maybe we should draw up a list of 'words we can't use'.
Lessee, light, darkness, 'Mother Nature', design. Now 'motor'?
The boneheads want to find some sort of allegorical underpinning to 'codewords', they can just sod off.
These people have way too much say in the world. Now I have to, in the words of Ari Fleischer, 'watch what I say'?
No thanks.
Free thinkers shouldn't have to moderate their language to communicate.
I probably wouldn't have used the term "motor" in this discussion, even though it is commonly used in the literature when discussing these things.
The word "motor" is used in the "literature" because that's what these things are.
Should we also stop using the phrase "motor neurons" or "motor paralysis"? When I was unable to move for nearly 2 years, it was due to "motor paralysis," and it had nothing to do with my car.
Anyhow, my favorite motor protein is kinesin. When I first tried to seriously study it in the early 90s, I found only 2 sites on line that mentioned the word. (Back in the days of FTP searches.) A few months after I handed in my paper, there were 7 sites that I could locate. A year later, I could turn up a few dozen references, then, shortly thereafter, more than 100. By the mid 90s, kinesin had a home page on the Web. I just did a Google search now and got 899,000 hits for kinesin.
I am truly grateful to people like PZ who put informative scientific descriptions and explanations on the web. And decent search engines, well Google has enhanced the quality of my life, that's for sure.
llewelly: PZ, the text in the image 'musclemyosin.jpg' has been ruined by jpegization -- even if I blow it up until it fills the screen it's completely unreadable.
Technically they are called the "head," "hinge," and "tail". I think this diagram has some adjectives added that are probably not that important. (like globular for the head)
The Vale Lab at UCSF has some great animations of these "motors"
(valelab.ucsf.edu) and in particular (valelab.ucsf.edu/movies/movies.html
Miko, I was just trying to learn something. Anyway, I am the first to admit that my cell biology is rusty. I just thought someone might have a good answer, but you are right, maybe I should look elsewhere. No need to overreact.
mndarwinist, the removal of part of the RNA before translation is known as splicing, and the removed part is known as an intron. Introns are found in some bacteria and archaea -- they are not unique to eukaryotes. Introns probably originated as self-splicing RNAs, which still exist today.
Introns are far more common in eukaryotes than in bacteria, and we do not know why this is. Many of the self-splicing introns in bacteria can copy themselves to elsewhere in the genome, which shows how they might have proliferated. One theory has to why bacteria have so few introns is that introns are very slightly deleterious, but because bacteria have huge populations, the introns are selected against. In larger organisms that have smaller population sizes, selection is less efficient and the introns would persist. Also, sometimes these introns have beneficial regulatory functions.
Hello
I do not many things about myosins. But if I do not make a mistake, myosins move in the same direction and they have a contribution in contraction.
Now my question is if they can pull muscles.
We know that in our body every contractions is beside pulling another muscle.
Thank you
Faezeh
What's so bad about "motor"?
There recently was a very good Nature paper on the latest hypothesis: the mitochondria introduced introns, which were originally transposons or something, and the only way to survive that was the evolution of the nucleus. It's explained in quite some detail. I just can't find the paper right now...
Namesake:
.. ,--Bacteria
.. |
---|
.. | .. ,--Archaea
.. | .. |
.. `----|
....... |
....... `--Eukaryota
Tree-thinking.
(Ignore the dots; they are supposed to be whitespace. Time runs left to right.)
F***! Why does the preview use a different font than the actual article! Screwed up the careful spacing. Well, fortunately not much.