Two of our favorite animations from WEHI. First, what it takes for chromosomes to condense, and we mean really *condense.* Second, the process of copying DNA. If you thought it was simple, look again. It’s like sewing and fly fishing put together, but on nanometer scale.
Back in the late 1980s and early 1990s, DNA sequencing was sweeping the scientific scene because of its power to answer a number of unsolved problems.
Cann et al sequenced mitochondrial DNA from around the world to show that all women were descended from a single woman who lived some time around 200,000 years ago. (Similar work was also done for the Y chromosome and the male lineage.) One of the possible interpretations of this study was that the single woman was Eve.
The scientist Francisco Ayala did not like this interpretation. To do him justice, it is indeed possible that there were many women alive at the time of the woman progenitor “Eve”, and that their lineages died out over time. Nontheless, Ayala set out to to not merely challenge but to disproveeven the possibility of an historical Eve (and Adam), using the same sequencing and phylogenetic analysis methods that Cann et al had used. For his study he chose to analyze a highly variable gene, HLA-DRB1, that is part of our immune system.
HLA-DRB1 is located in the the human leukocyte antigen (HLA) complex. Most of the genes that encode the proteins involved in immune defense are located here. Some of these genes are highly variable in sequence, with hundreds of alleles each, including HLA-DRB1.
The variation of HLA-DRB1is mostly limited to one small domain of the protein, called the peptide binding site (PBS). The PBS is where the rubber meets the road for recognizing and presenting foreign proteins to the immune system. Variation in the PBS increases the chance that at least some individuals in the population will survive a new parasite or disease; one of these proteins may have a PBS with the right sequence to bind proteins from the attacker. That HLA protein can then direct the immune system to search and destroy anything carrying those foreign proteins.
Ayala sequenced the DNA encoding the PBS of HLA-DRB1 precisely because this gene has hundreds of variants in the current population. He compared DNA from many Rhesus macaques, chimpanzees, and humans, and based on those sequences, he constructed a phylogenetic tree—a tree intended to show the evolutionary history of this gene.
His conclusion? To account for the genetic diversity, there had to be at least thirty-two separate lineages of the gene at the time chimps and humans diverged from each other. And he explicitly argued that this ruled out a single Y-chromosome Adam and mitochondrial Eve.. as our original progenitors
But this wasn’t the end of the story. A few years later another group headed by Tomas Bergström challenged Ayala’s work, saying that he chose the wrong piece of DNA to study. The PBS sequence was inappropriate because it suffered from a high mutation rate and a high rate of gene conversion, both of which would cause an overestimation of the number of lineages for this gene.
Bergström’s group sequenced a neighboring region of the same gene that should not have these problems. They found that the estimated number of HLA-DRB1 lineages dropped from thirty-two to seven.
Now here’s where it gets interesting. The same group later sequenced a number of individual HLA-DRB1 genes again, but this time they sequenced the whole gene, a monumental task given its size. Guess what they found? Only four lineages predate the split of chimps and humans. A fifth arose about 3-5 million years ago.
Sequencing the whole gene from many individuals gave them more complete data, and permitted a finer resolution of the sequence comparisons. It also revealed a number of very interesting things. The introns (the non-coding portions of the gene that get spliced out before it is turned into protein) showed that the four lineages appeared to have been separate for a long time, based on the differences between them. It also showed that there had been an explosion of genetic diversity about 500 to 350 thousand years ago. It was about that time we went from a few lineages of HLA-DRB1 to many, resulting in the incredible diversity we see today.
Let me restate this in case you have missed it. Four lineages of this gene appear to be ancient, because they are so different from one another. But derived from each of those lineages are many, many alleles produced by some process that generates diversity fast, These newly appearing lineages tend to be more similar to one another, indicating that they are young. Surprisingly (there’s that word), their diversity appears to have arisen less than half a million years ago. This result has challenged the strongly held views of some immunologists, and is causing a re-evaluation of the field.
Here are a few take-home lessons:
1. Scientists would be wise not to make strong claims on incomplete data.
2. Science does tend to be self-correcting in the long run.
3. The diversity of the human HLA complex is not due to the ancient preservation of many lineages. Rather, most of the variation is recent, and comes from only four lineages.
4. From thirty-two to seven to four. That’s a remarkable journey, one that was entirely unexpected (there’s another of those words). Four alleles can be carried by just two individuals.
Ayala’s conclusions were premature to say the least, and his argument against Adam and Eve has now been dismantled. In addition, the new evidence has indicated there must be a new explanation for HLA complex diversity.
As to the reality of Adam and Eve, I leave you to draw your own conclusions. But don’t be hasty. There’s a whole genome yet to explore.
About forty years ago, a biochemistry professor told my class that now that the genetic code had been worked out and the lac operon discovered, the only thing left for us students was to work out the details. Boy, was he wrong!
If there’s one thing I’ve learned over the last forty years, it is that every ten years or so the biological apple cart is upset, and a long-established “fact,” an assumption based on incomplete knowledge, is proven to be wrong.
I am sure you can find textbooks that still include some of these old “facts.” Below is a partial list of the “facts” that have had to be revised, and some that are still under discussion.
1. Old fact: DNA is stable and genes don’t hop around.
New discovery: Mobile genetic elements can hop from place to place in the DNA, duplicating themselves and changing gene expression. Sometimes they carry surrounding genes with them.
2. New “old” fact: Mobile genetic elements are selfish DNA that replicate themselves without benefit to the organism, thus cluttering the genome with garbage.
New discovery: Mobile genetic elements appear to be involved in the regulation of many important genes, and their distribution in the genome is nonrandom.
3. Old fact: A gene is an uninterrupted stretch of DNA that encodes a single protein. Genes are arranged like beads on a string.
New discovery: Genes in eukaryotes are interrupted, sometimes multiple times, by non-coding sequences called introns. The introns get spliced out of the messenger RNA before the message is translated.Because of splicing, one gene can produce many different but related proteins.
New discovery: Genes can overlap one another on the same stretch of DNA, on the same strand or on opposite strands. Thus one piece of DNA can produce multiple different proteins.
Take home message: 1 stretch of DNA ≠ 1 gene ≠ 1 protein
4. Old fact: There are only 3 forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.
New discovery: New classes of short and long RNA transcripts serve to regulate gene expression.
5. Old fact: Pseudogenes are useless broken remnants of former genes.
New discovery: Not all pseudogenes are useless. Pseudogenes can be transcribed, and their products can be used to regulate the expression of their full-length sister genes. Related to #4.
6. Old fact: The genome is full of junk, the remnants of wasteful evolutionary processes and selfish DNA (see #1, #2 and #5 above).
New discovery: ”Junk” DNA isn’t junk after all. It has many important regulatory functions in the cell.
Revolutionary discoveries like these often happen when someone tries something new, stumbles across some contrary evidence, and begins to question the validity of an established “fact.” The results have been astonishing—and have even won the Nobel Prize. Because of these discoveries we have gained a new and better, though still imperfect understanding of biology
Why should we still have the “facts” wrong? After all, we’ve been studying biology for 60 years after the discovery of DNA’s structure, and 50 years after the code was worked out.
Perhaps a better question would be, “Why does biology have the ability to surprise us?” It’s because life is much more sophisticated than anything we can imagine. We look at biology from our very limited perspective, and at almost every turn we are puzzled or amazed. You can even read it in the understated, carefully couched language of published articles, where words like “surprising” or “unexpected” appear often.
Remember that biochemistry professor who claimed that all the important work in biology was done? He also said we’d never find gears or wheels in biology. Poor guy!
You’d think that scientists would be more cautious about our pronouncements if we can be so wrong. But we are only human, like everyone else, and our accepted “facts” are often deeply entrenched in our thinking. In truth, though, only one rock solid “fact” exists—that some time in the not too distant future a strongly held “fact” will be proven mistaken.
I’m not a person who enjoys roulette. That’s because over the long haul the house always wins. I don’t believe enough in luck to want to gamble on placing just the right bet.
Yet it seems some scientists think an incredible string of luck, analogous to making a series of very lucky bets, is the explanation for why we are here.
Here’s what I mean. In a paper just published in Nature, “Historical contingency and its biophysical basis in glucocorticoid receptor evolution,” Michael Harms and Joseph Thornton described creating an “ancestral” form of a steroid binding protein, and then testing thousands of evolutionary paths forward from the ancestral form to the present day protein. They found that two “extremely rare” mutations were absolutely required, that is, they had to be in place before the protein could ever evolve the ability to bind cortisol. Yet these two specific mutations had no beneficial effect on the protein by themselves, and so had to appear by chance!
Tracing these alternative evolutionary paths, the researchers discovered that the protein - the cellular receptor for the stress hormone cortisol - could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These “permissive” mutations had no effect on the protein’s function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein’s modern-day form to evolve. [Emphasis added.]
"This very important protein exists only because of a twist of fate," said study senior author Joe Thornton, PhD, professor of ecology & evolution and human genetics at the University of Chicago. "If our results are general — and we think they probably are — then many of our body’s systems work as they do because of very unlikely chance events that happened in our deep evolutionary past," he added.
What Thornton’s saying, I think, is that many mutations had to happen, with no help from natural selection, in order to make other mutations possible. And all these mutations somehow came together to make the proteins necessary to build functioning organisms. In other words, we were incredibly lucky.
Design is the better explanation, though. Think of it this way. When playing roulette, if you are looking for a specific number (mutation), you may have to wait a very long time to win your bet. You could then try again for another win, but you’d probably have to spin a long, long time to get the next winning bet. In fact, if you did keep on winning, spin after spin, everyone would wonder how you were cheating. Repeated bucking of the odds is always a sign of intelligent agency. Just ask the casinos.
Would it help to have millions of roulette tables, to continue the metaphor, all spinning at the same time to increase your chances at winning? Perhaps, but in biology, it’s not enough to have the lucky neutral mutation(s) arrive. Things get lost more often than they last. Also, eventually all those scattered winnings from different tables have to be in one person’s pocket. All the various permissive mutations have to come together in one organism.
That might sound trivial if everything was linear and tidy, like repeated spins of a roulette table, but evolution is anything but. Multiple incipient adaptive traits are being sampled all at once, each composed of various mutations, none of them beneficial yet. We have to abandon the roulette image here because it’s too simple, too linear. Evolution is more like a vast sea of unrealized possibilities with someone dipping in a ladle and pulling out a sample to drop into the next sea. Getting a workable combination by chance is unlikely to say the least.
United States Postal Service Truck by Alexander Marks; Public Domain
The manufacturing system of cells is elegantly designed to produce proteins and other complex molecules, which must then get to the right locations. Small cells like bacteria can probably do it by diffusion, but larger eukaryotic cells need a directed delivery system. As a result, eukaryotes have efficient motors to carry cargo, and a “postal system” to direct the motors to the appropriate destinations.
Destinations differ. Some cargos go to the growing front end of a migrating cell. Others must travel the length of a neuron’s long axon to get to their destination. And some have to be exported outside the cell. As an example, epithelial cells have three distinct surfaces, top, bottom, and sides. Each surface needs a different set of molecules delivered to it. Without this differentiation, tissues and organs made of epithelial sheets could not form or function properly,
In embryos, special “determinants”, either protein or RNA, have to be delivered to the right location in the developing egg or embryo. Once again, without these determinants the body plan of the nascent embryo is disturbed.
How is all this coordinated? How does the cell know where to deliver its products? What is the address system? Where precisely is the map that matches all these addresses? And who is the postman that matches address to map and delivers the package to the right address?
There are three “postmen,” dynein, kinesin, and myosin. For delivery to the periphery of the cell, the job is usually done by kinesin. Kinesin is composed of two parts— two heavy chains that form the walking two-headed motor and its long coiled stalk, and two light chains, that bind at the end of the stalk and make a fan-like tail.
It has long been thought that the light chains are involved in binding to and perhaps distinguishing among the many cargos that kinesin delivers. It is also thought they play a regulatory role for the motor domain. If the kinesin heavy chains have no attached light chain, they fold on themselves and inactivate the motor. So the light chains function like an on-off switch for the motor, which helps to conserve energy. They may also serve to promote interaction and cooperation between dynein and kinesin.
There are multiple versions of the light and heavy chains. Some are generalists, and some are specific to particular cell types. We now know that defects in different kinds of heavy and light chains are associated with particular diseases, most notably, Alzheimer’s.
What we do not know is how everything gets sorted to the right destination. There is much more work to be done, but progress is being made in determining some of the linking ”address” proteins that bind the light chains.
This system is present in most if not all eukaryotes. In fact, it appears to date back to the first eukaryotes. Let’s consider how this system might have come about. All parts are necessary for it to work. To return to our metaphor, if the postman just started transporting things at random, what benefit would that be? Yet address molecules are of no use without a postman, or without paths to travel on. Thus directed transport requires a complicated set of interacting parts, each of which is essential.
Without these motors and their interacting proteins, migrating cells wouldn’t have the materials they need to move forward. Axons would die from lack of mitochondria and/or they would send signals very inefficiently. Epithelial cells would have their bottoms and tops confused. And embryos? A mess.
Oh, and I haven’t mentioned that both kinesin and dynein are essential for chromosome movement and spindle formation during cell division.
Amazing. Hard to sort out how it happened, isn’t it?
Perhaps you’ve seen the video from Discovery Institute of the miniature walking machine known as kinesin. This microscopic marvel helps to get the cell’s protein products distributed to their final destinations, among other things.
Kinesin’s movement is extremely efficient, and by itself is a wonder. But there’s another wonder. A single kinesin can pull its cargo at up to 800 nanometers per second along its microtubule highway, depending on its load and the amount of ATP available. That’s almost a micron per second. To give you a sense of scale, one bacterium is about a micron in length, and a typical animal cell is roughly 10 microns. That means that, under optimal conditions, and if kinesin is unobstructed, it could travel the length of an average cell in about 12.5 seconds. That is fast. If it partners with other kinesin molecules, it can move even faster.
This is a good thing for our neurons. A neuron has its nucleus and biosynthetic apparatus in its cell body. This where the proteins and organelles that the neuron needs are made. But these proteins and organelles are used out at the very tip of a long thin process called an axon, which extends from the body of the neuron all the way to the place it sends its signals.
Different kinds of neurons. Image by Jonathan Haas via Wikimedia Commons
In the brain there are billions of neurons with axons connecting one region to another (the different kinds are shown above). In the peripheral nervous system, axonal processes can reach up to several feet in length. For nerves running to your toes, for example, axons must reach all the way from your lumbar spine. Therefore anything delivering essential items down axons needs to be fast.
How do the proteins and organelles get from where they are made to where they are used? And how do things that need to be recycled return to the cell body? It’s by means of kinesin for outward bound travel and another motor protein called dynein for inward bound travel. Remarkably, dynein and kinesin cooperate, rather than compete—otherwise there would be a constant tug of war in the cell. They “know” where packages are meant to go, and which motor protein should do the job. How that happens is a whole other story.
This isn’t just abstract stuff. Many neurodegenerative diseases have been linked to mutations of kinesin, including Alzheimer’s disease. So this little workhorse of the cell is not only a marvel, but essential.
If you’d like to see a short time-lapse video of axonal transport in hippocampal neurons, click here.
Finally, in order for kinesin to do its work, we need the motor protein itself, the microtubule highway it walks along, and some mysterious means of connecting and directing where its cargos get carried. This whole system appears to be essential for a variety of eukaryotic cell functions; at least eleven kinesin families appear to have existed in the putative last common ancestor for all eukaryotes. Yet evidence for kinesin motor proteins in bacteria is sketchy at best. Thus we have another complex system necessary for eukaryotic cellular function that seems to have appeared out of nowhere.