Posted on 01/14/2002 3:01:36 PM PST by Karl_Lembke
By Barry A. Palevitz
One of the enduring questions in biology is how eukaryotic cells arose from prokaryotic ancestors at least 2 billion years ago. Besides differences in genome organization, eukaryotic animals, plants, and fungi possess a much higher degree of cellular compartmentation in the form of membrane bound organelles than their distant bacterial and Archaean cousins. But how did such a plethora of cellular domains, each with a discrete role in metabolism, evolve?
To the extent that science proves anything, it answered the question for two eukaryotic organelles a long time ago. Mitochondria and chloroplasts evolved from endosymbiotic associations between an ancestral host cell and smaller prokaryotic partners. In the case of chloroplasts, the symbiont was a photosynthetic cyanobacterium; for mitochondria, most likely it was ana-proteobacterium.
The cytoplasm of eukaryotic cells is like chicken soup-it's chock full of organelles suspended like chunks of assorted vegetables and noodles in cytosolic broth. The broth also contains filaments of various dimensions that collectively comprise the cell's cytoskeleton. Like the bones of a large animal, the cytoskeleton provides a structural framework lending shape to cells and against which enzymatic 'muscles' work to elicit movement. That's how amoebae migrate, algae swim, stem cells divide, and cytoplasm streams relentlessly up, down, and across plant cells.
While the cytoskeleton is as much a hallmark of eukaryoticity as any mitochondrion or chloroplast, the origin of its filaments in deep time is more mysterious. Biologists assumed that genes for cytoskeletal proteins arose from prokaryotic precursors, but evidence in favor of the hypothesis was scarce, until recently.
Tubulin First on Stage
Microtubules comprise one component of the cytoskeleton responsible for a variety of movements including mitosis and meiosis. The 25 nm tubes consist of dimerica- and b-tubulin subunits that share about 40 percent sequence homology. Another form,y-tubulin, functions in microtubule formation.
But where did microtubules come from? It now appears that tubulins share a common ancestor with a protein called FtsZ, a key player in bacterial cell division.1 FtsZ is also present in plants, where it functions in chloroplast division,2 and a similar protein associates with mitochondria, at least in one alga.3 FtsZ polymerizes into filaments in the test tube in a process dependent on GTP. The same nucleotide is required for tubulin assembly into microtubules.1
Tubulins and FtsZ are clearly related, judging from similarities in three-dimensional structure. And although the proteins share only about 15 percent amino acid sequence identity overall, they're much more similar at the local level, particularly at the domain responsible for binding and cleaving GTP.4,5
Actin Into the Fold
Like the tubulins, actin-another essential component of the eukaryotic cytoskeleton-is a globular protein that binds nucleotide, in this case ATP. As actin monomers polymerize into 6-nm-wide microfilaments consisting of two helically wound protofilaments, the ATP, situated in a deep enzymatic cleft between two halves of the protein, hydrolyzes to ADP and inorganic phosphate.
It turns out that actin shares its ATPase domain with a family of proteins including hexokinase, the enzymatic kick starter of glycolysis, and several bacterial proteins. One of them is called MreB, a protein essential for generating or maintaining the rod shape of many bacteria. By examining structural similarities between eukaryotic actin and MreB from Thermotoga maritima, a research team at the Medical Research Council in Cambridge, England recently concluded that the two proteins are more closely related to each other than to other members of the family and undoubtedly share a common ancestor.6
The group showed that the three-dimensional shapes of actin and MreB are so similar they can be superimposed. The analogy with tubulin/FtsZ goes even further. Both proteins share considerable amino acid homology at several key sequences surrounding the ATP binding site, again situated deep in a cleft between two halves of the folded polypeptide chain.
Under the right conditions, MreB polymerizes into protofilaments that pair up lengthwise. The protein subunits are spaced about the same distance apart along the filaments as in polymeric actin, but MreB double filaments aren't nearly as helical.
The similarity between MreB and actin doesn't stop at structure and sequence. In a paper published earlier in 2001, a research group led by Jeffrey Errington at the University of Oxford, U.K. visualized MreB in the rod shaped cells of Bacillus subtilis using fluorescence and electron microscopy.7 MreB forms filamentous bands that encircle the cell in low helices, like reinforcing hoops. In an essay accompanying the Cambridge group's article, Duke University cell biologist Harold Erickson calculated that each band contains 10 protofilaments.8
When Errington's team genetically deprived cells of functional MreB, they became spherical. A search of genome databases showed that MreB is present in bacteria with nonspherical shapes, including rods. It's absent in spherical cocci. In other words, MreB has a cytoskeletal function. "I think it is quite convincing that MreB is the actin progenitor," says Erickson. "A key step, still unknown, going from bacteria to vertebrates is to develop a mechanism to make the double-helical actin filament from the single MreB protofilament structure."
More Acts to Follow
The story doesn't end with MreB; there's more to find out. Scientists want to know if MreB is also present in eukaryotes-associated with mitochondria and chloroplasts-as is FtsZ. According to Katherine Osteryoung, a plant biologist at Michigan State University in East Lansing who identified two FtsZ genes in the mustard plant Arabidopsis,2 "there's no obvious indication of MreB in plants that I've found or am aware of."
Actin normally functions along with the motor enzyme myosin to produce cellular motion, while microtubules utilize two other motor families called dynein and kinesin related proteins. Researchers now wonder whether MreB and FtsZ work in conjunction with bacterial motors. According to Erickson, "none have been turned up in genetic screens for cell division (or other activities), and none have been identified by sequence gazing. My bet is that kinesin and myosin evolved in eukaryotes, after the evolution of microtubules and eukaryotic actin filaments."
Still, Osteryoung is pleased with the latest results: "To someone interested in these issues, establishment of the prokaryotic origins of two major eukaryotic cytoskeletal proteins is enormously satisfying. I look forward to the day when evolutionary intermediates... from MreB to actin and FtsZ to tubulin, perhaps awaiting discovery in some obscure and primitive eukaryote, will more fully reveal the evolutionary steps by which key components of the eukaryotic cytoskeleton acquired their present-day structures and functions."
Barry A. Palevitz (palevitz@dogwood.botany.uga.edu) is a contributing editor for The Scientist.
References
Microtubules, which play a part in moving parts of the cell from place to place, turn out to share a common ancestor with another protein which a key player in bacterial cell division in bacteria, and chloroplast division in plants. A similar protein has been found in the mitochondria of at least one alga.
The components of microtubules and the earlier proteins "are clearly related, judging from similarities in three-dimensional structure. And although the proteins share only about 15 percent amino acid sequence identity overall, they're much more similar at the local level, particularly at the domain responsible for binding and cleaving GTP."
This is only to be expected from evolution -- the sites that interact with other molecules will be more sensitive to changes, and amino acid sequences are expected to be conserved there. Changes away from these sensitive regions are less significant, as long as the overall shape of the protein remains the same.
Actin is another essential component of the eukaryotic cytoskeleton--a globular protein that binds nucleotide, in this case ATP. In the cell, it cleaves ATP into ADP and phosphate. (It is also a major component of muscle tissue, forming part of the machinery that allows muscle fibers to contract.)
Actin turns out to be related to a whole family of proteins, including one which is involved in glycolysis, the basic metabolic process in anaerobic life. Another related protein generates and maintains the rod shape of bacilli. Structural similarities hint that actin is more closely related to the bacterium Thermotoga maritima, and may share a common ancestor with the protein in that bacterium.
Interestingly enough, we have many sets of protein which are very similar in shape and function, but which differ more than a little in the details of their composition. The differences that turn up are orderly enough to look like family resemblances, and can seem to indicate a family of descendants of a common ancestor. Again, evolution would predict this sort of distribution. One member of the family was incorporated into eukaryotic cells, and its protein was passed down to all its descendants. Other members of that ancestral family were already slightly different from the ancestor of eukaryotes, and to these differences were added other mutational changes.
The protein in the nearest relative, Thermotoha maritima, has slight differences from modern actin because, although the ancestral bacillus protein and the ancestral actin were once identical twins, they have diverged through random mutations.
When scientists investigate the intricate molecular machinery in cells, they find that these machines, rather than springing up fully-formed out of nowhere, there are numerous relatives and precursors in other organisms, and sometimes in the same cell. The development of cellular machinery is not so much an account of complicated machinery appearing out of nowhere, but more of existing bits and pieces being fitted together to solve different problems.
And once again, pay particular notice to how evolution is treated in this article. It is in no way a sense of "Hey, guys! It happened!". Instead, it's a matter of, "We've been pretty darn sure it happened; this is how it happened in this case." The only people caught up in whether evolution can be "proven" seem to be the Intelligent Design / Intelligent Origin crowd and the Creationists.
Osteryoung states unequivocally that these eukaryotes descended from prokaryotes. Yet there is no proof of this contained in the article, which only points to certain protein similarities. "Looks like" is not the same thing as "comes from."
Notice the tacit assumption? The very first sentence of the article does not ponder whether this occured or how it might have occured, but takes it as a given, the only task being how to demonstrate the mechanism.
The very next paragraph demonstrates the same confusion between what has been demonstrated and what has merely been theorized. The author even admits that the "evolution" of the chloroplast only "most likely" from the ana-protobacterium. Doesn't sound like much of an "answer" to me. Sounds more like theory or conjecture being represented as a settled matter.
Aren't they all so silly, those biologists?
Of course, Earth just happened to be in the right location and distance from the Sun; geologic processes just happened to be in the correct sequence; just the right amount of "star matter" and radiation was allowed to fall upon proto-Earth; just the right amount and mixtures of chemical "soup" happened to occur on Earth. ad nauseum.
Yes, it all happened just right and "POOF!" Life, as we 'know' it............evolved!
WOW!
No where else(?) can evolved sentient creatures ponder their own existence and "creation".
It's freaking amazing, eh?
Why provide a number when it shows a difference and only a vague "much more" when the similarity is purported to be important? It seems to me that the number, if significant should be at least 30%, given my interpretation of much and the general chimp/human genome simularity of ~98%. (it also matters as to the definition of local)
And although the proteins share only about 15 percent amino acid sequence identity overall, they're much more similar at the local level, particularly at the domain responsible for binding and cleaving GTP.
Why provide a number when it shows a difference and only a vague "much more" when the similarity is purported to be important? It seems to me that the number, if significant should be at least 30%, given my interpretation of much and the general chimp/human genome simularity of ~98%. (it also matters as to the definition of local)
It's very easy to count matching and non-matching amino acids. How do you quantify similarity of shape and structure?
I don't think they meant to quantify those attributes, rather I thought they meant the sequence of the proteins local to the active parts of the structure, the bonding sites for instance. At those critical points the sequence would be more sensitive to change and likely to be selected out/in.
Yes. After the first one, I got a message telling me the page was not available. It didn't appear when I refreshed the forum, so I paged back and hit "post" again.
Pile on as much irony as you like. The point is, real scientists, doing real research, don't care what you believe. Evolution works. Intelligent Design/Intelligent Origin Theory (IDIOT) doesn't.
Real scientists don't waste their time proving quantum mechanics, general relativity, the germ theory of disease, or the notion that the earth is round, either.
How do you quantify similarity of shape and structure?
I don't think they meant to quantify those attributes, rather I thought they meant the sequence of the proteins local to the active parts of the structure, the bonding sites for instance. At those critical points the sequence would be more sensitive to change and likely to be selected out/in.
I suspect you're right. But your original question was,
Why provide a number when it shows a difference and only a vague "much more" when the similarity is purported to be important?
The point is, it's very easy to quantify amino acid substitutions, and the differences and similarities involved. It's considerably less easy to quantify differences in shape and configuration.
For example, how would you handle the task of rating clouds to see whether they look more like Thomas Jefferson or Madonna? How would you assign a numerical value?
ahem cough snicker.
[CLICK HERE] for the other thread with more responses.
So, why is it that an infinitely more complicated pattern and structure in biology must have happened by chance?
Evolution, while claiming to be intellectual and logical, seems very illogical to me.
The simplest would be a 2D ratio of the area covered by the purported image to a circle circumscribed about a central point determined by the midpoint of the long axis of the image in the cloud. This ratio would be compared to a like ratio determined for the image of each (in)famous persona. The closest match determining the Madonna-esness or Jefferson-esness of the cloud image. (you actually are stating the problem as it relates to the proposed automatic airport identity software. The problem is definitely solvable)
So, why is it that an infinitely more complicated pattern and structure in biology must have happened by chance?
They're basically looking for a pattern that's not already seen in nature - isn't that right, RA?
(And there's the rub re: proteins. Protein structures & sequences are seen in nature!)
So, why is it that an infinitely more complicated pattern and structure in biology must have happened by chance?
Actually, what they're looking for is not so much complexity as regularity and patterns. The most complex signal there is is random noise. The heavens are filled with random noise, but no one attributes its complexity to intelligence or design.
Evolution, while claiming to be intellectual and logical, seems very illogical to me.
OK, let's see your logical analysis.
That might be an interesting application. Maybe some researchers will try it in the near future.
It would be interesting to see this software applied to this sort of research. A decade ago, protein folding was a hot research topic, and they were trying to work out approaches to it. I haven't followed the research at all.
For SETI research, we are looking for an extremely narrowband CW signal. This alone signifies a non-natural origin.
Not so much a pattern, but a type of signal not found in nature; narrowband CW. :)
IIRC, you recently explained the reasoning behind this. Isn't it both because narrowband CW is not found from known natural sources, and because it is found from known intelligent sources (human-made radio stations)?
You are most correct! :)
Based on what we actually know at this point, it appears we are alone. It's all ours.
Sagan has passed on and taken his purple-hazy visions with him. The peace and quiet we now experience allows us to look around with fresh eyes. We see no evidence whatsoever of extraterrestrial civilizations. None. Zero. Nada.
Works the other way as well. To say there must be ET is just as baseless.
Not talking odds, not talking feelings. There is no evidence of ET. Not the same as saying there is no ET, just saying there is no evidence of ET. Not like saying there must be ET when there is no evidence of ET.
No, to say right NOW that there are no other intelligent civilizations out there besides ourselves, is just arrogance talking, not scientific proof. ...... I am certain that there are others out there, it's just a matter of time.
Beautiful! I don't even have to compose my own answer! Let me give it a shot: Soon, we shall know for sure if there is a God out there, but to say now, that He does not exist, is speaking without any facts.
No, to say right NOW that there is no God out there is just arrogance talking...I am certain that there is a God out there, and it's just a matter of time. Many of us know now that He lives, but it is just a matter of time (death) before everyone knows.
God is within and without. This is not a belief, I know this. So do you.
But . . .
We're talking ET here.
So we can say now that two proteins must be related because they share a similar function in one domain and they have a whopping 15% homology!
I've done a little study of my own. I found that a yugo shares many of the same functions as a Honda Civic. They both have four wheels, a motor, a steering wheel, a gas pedal, a brake, headlights, etc. In fact, I'm sure that they share more than a 15% homology.
I have concluded that long ago, a steel mill blew up and over billions of years, yugos evolved. After another billion years, Honda Civics have evolved from yugos. If we carry this evolution even farther, we get a Hummer!
All organisms share some sort of homology. If one function is to be performed (like the cleaving of GTP), it would make sense that God used a very similar-looking molecule to accomplish the task.
The development of cellular machinery is not so much an account of complicated machinery appearing out of nowhere, but more of existing bits and pieces being fitted together to solve different problems.
While this article discusses protein similarities, the question still remains: what is the MECHANISM of the change? How long did it take? Is anyone in control of it? I believe that God has taken these bits and pieces and put them together to create distinct organisms. These organisms all share the same building blocks and need to perform some of the same functions, so of course some of the molecules will look similar. This is analagous to the car example. A Honda Civic shares a lot of the same parts with a Honda Accord. It does not mean one "evolved" from the other, it means they had the same DESIGNER!
Think about it. If God didn't design this world and its inhabitants so that they would be somewhat similar, it wouldn't function the way it does. Just because things have similarities does not mean that they were not designed that way on purpose. If God didn't use the same 20 amino acids to make up all the proteins in this world, we wouldn't be able to eat anything.
The design of this world is so intricate and ingenious that I am in awe. I can't reconcile the word "accident" with the things I see happening in the human body, let alone the interworkings of the world with its inhabitants and the inhabitants with each other.
Actually, both would work almost equally well as a paradigm to discuss and categorize biological data.
Your earlier comments are quite astute ("The point is, real scientists, doing real research, don't care what you believe.").
Nor do they care what a bunch of religious zealots who take biology and evolution as a substitue religion believe.
Yes and no. When it comes to proteins that are as separated as those from bacteria and mammalian it can be difficult.
How do you quantify similarity of shape and structure?
I am not sure if this is a rhetorical question or not. If so what is your point? If not, I will address it.
No, he's right - you sequence the amino acids and count the matches. I've done runs on proteins from organisms as different as E. coli and rhesus monkeys. This does not, however, measure secondary and tertiary structure, which is what you really need if you're to determing biological activities, but the amino count won't get you there by itself.
Sorry to ruffle your feathers, but you did state your belief as declarations of fact (NO WAY..., etc.)
As for God using evolution to create - that's a tough sell. If we (man) are nothing more than upgraded monkeys, then there is really nothing special about us. But He says He made us in His image. He loves you and me, no matter if anyone else does or not.
Good comments. The answer is that when comparing related proteins from very different organisms the similarity can decrease to 15% or so, yet there is still a recognizable relationship based on structure and function. Using the design paradigm, rather than evolutionary one, it would be that the watchmaker used a phillips head screw in one case but a thumbtack in the other.
The ape and man were made with phillips head screws, maybe a little different in width or size, but very close. The bacteria does the same thing with a thumbtack. That's the analogy. The head and pin of the tack and the screws are different by a fair amount but there is still a conserved shape and function we can see. That is the 15%.
On the subject of sequence similarities, it can be tricky. There are amino acid comparisons (or protein sequence) and DNA sequence similarities. DNA (nucleic acid) codes for the amino acids and it takes three individual nucleic acids to code for one amino acid. There are more than one three letter codes for each amino acid as well (with one excpetion -- can the fundie evolutionite cultists answer the question which one? Probably not). This degeneracy of coding means that a peptide sequence can theoretcially be a 100% match, but the gene coding for them will not be.
For example, the three letter codes for valine are:
GTT
GTC
GTA
GTG
You'll note they all have GT as their first two bases.
So, one DNA sequence might be:
GTTGTTGTTGTT
and another
GTAGTAGTAGTA
Comparing them we have:
GTTGTTGTTGTT
GTAGTAGTAGTA
Red and blue being the bases that differ. Only 8/12 are identical. That means a DNA similarity of 67%.
But all the triplets code for valine, so it is a 100% match at the protein level.
No. Run some blasts or simple seq aligns with disparate proteins. You'll not get the right matches in many many cases.
Some random sequence might have a high match in an unconserved region and skew the alignment. And the differences in size always make it hard to know where to begin the alignments, where the gaps are.
heck, run programs with slightly different algorithms from different labs and you'll get different alignments and gaps etc...
Of course it is easy to line up two sequences and count matches. But if they differ by a lot there is a lot more to it than just slapping them next to each other.
Take for example a hypothetical protein with two transmembrane domains. One is in bacteria, the other mammals. The latter is 400 aa and the former 250. Line them up from their amino terminals and look at the matches -- it means nothing. I shouldn't have to have to tell you this.
Oh, lordy, tell me about it! But you're right, and that was my point - you can do a crude count and get numbers and compare them and you really haven't measured anything much. Before we really get an idea of the evolutionary implications (if any) of this sort of research we're going to have to know a great deal more about why things fold up the way they do and stick to what they stick to.
Nobel time prize for that.
This kind of recurrent objection to the plain evidence always makes me wonder about what self-esteem problems religious people suffer.
I mean - we've gone in just 6,000 years from unable to make written language to sending probes out of our solar system, unlocking the genetic code of life, probing the subatomic and mapping the galaxy. Not to mention whipping most diseases, hunger, increasing personal liberty, etc etc etc. Then there's all that philosophy, morality and ethics we've developed over the millenia that increasingly focuses on individual liberty rather than service to king or state.
Hell, I'm practically exploding with pride. If that doesn't make us pretty freaking special, I don't know what would.
Am I the only one thinking this?
They're basically looking for a pattern that's not already seen in nature - isn't that right, RA?
Not so much a pattern, but a type of signal not found in nature; narrowband CW. :)
As soon as one is found, though, it'll be carefully examined to see if there's any possible natural explanation for it.
Recall pulsars.
And Sagans hay vision as you call it, is based on statistical analysis, which is a pretty good science. Otherwise gambling wouldn't make the house money.
No, to say right NOW that there are no other intelligent civilizations out there besides ourselves, is just arrogance talking, not scientific proof. Besides, we are out on the edge of the galaxy, most stars are towards the middle of the galaxy, so it may be a while before we detect anyone else.
While we're looking at the statistics for the number of possible civilizations in the galaxy, we should also think about the window of opportunity for civilizations to make contact with other civilizations.
If the life span of a civilization is less than a million years, then our chances of detecting anyone else may be few and far between. There might be a hundred civilizations that have formed in our immediate neighborhood, but the most recent may have collapsed thousands of years ago. Any radio signals we might detect are now well out of reach....
I am certain that there are others out there, it's just a matter of time. Statistically, it's almost impossible for us to be alone in the universe.
I'm for hypothetically dissecting the mysteries of origins as far as possible, and yet I still wish to hold the mystery of creation dearly. Panspermia is a worthy contender, as is the quantum multiverse concept, at least to my ways of thinking at this time.
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