In the 1960s and 1970s, we began to learn about specialized recombination processes independent of genetic homology: chiefly, virus insertion and excision by site-specific recombination and transposition (Bukhari 1977). These were different from the familiar homology-dependent recombination used to establish genetic maps. Because they were new, there was a tendency to name homology-independent processes "illegitimate recombination," implying they were very specialized and not of general importance. Today, of course, we know that the movement of mobile genetic elements by "illegitimate recombination" is ubiquitous and of major evolutionary importance.
We have also learned that cells can use "legitimate" recombination in many different ways. It begins with a double-strand (DS) break in one of two homologous DNA molecules. When such breaks occur accidentally, they trigger homologous recombination for DNA repair.
In many situations, cells need recombination when no accidents have occurred. They possess special enzymes, endonucleases, that make DS breaks to initiate the process. For example, homologous recombination holds chromosome pairs together in meiosis. My University of Chicago colleague, Rochelle Esposito, and her students discovered that there is a special endonuclease, Spo11, that makes the essential DS breaks. Without Spo11, yeast and other organisms cannot carry out a normal meiotic process to produce haploid spores or gametes.
Spo11, like all endonucleases, cleaves preferred sequences. So there is a non-random pattern to the sites where homologous recombination occurs preferentially ("hotspots") in yeasts, plants, and animals.
A very recent paper illustrates another kind of hotspot control. Mouse cells have a special chromatin-binding protein that alters recombination hotspots: it binds to highly evolved genome expression signals in mouse DNA and protects them from disruption by homologous recombination. Without the protective binding protein, they become recombination hotspots.
The ability to target homologous recombination by DS breaks has also been utilized by different kinds of cells as a means of altering the proteins they express. In this way, some cells use "legitimate" recombination in the way other cells use "illegitimate" recombination. The first example of this specialized use of homologous recombination was in yeast sex change operations.
When yeast cells undergo meiosis, they produce four haploid spores. Haploids have one copy of each chromosome, not two. Spores can reproduce as haploid cells but are more sensitive to DNA damage. Diploid cells with two copies of every chromosome are less sensitive because damage to one copy can be repaired by recombination using the second copy. Thus, yeasts benefit by propagating as diploids, and most yeast in nature are diploid.
Haploid yeasts become diploids by fusing with cells of opposite sex, or "mating type." Sometimes this occurs between adjacent spores of opposite mating type following meiosis. But if one spore becomes isolated, it only has single mating type. How can it become diploid? The answer is to undergo a sex-change operation or "mating-type switching." The switch produces haploid cells of the opposite mating type so that fusion and diploid formation can proceed among the descendants of a single haploid spore.
In both budding yeast and fission yeast, sex change occurs when copies of epigenetically silent mating type information replace expressed mating type information. The substitution occurs by a directional form of homologous recombination called "gene conversion," where information at one site is copied into another homologous site. Although the sequences for the two mating types must be different, the silent region and the expressed region to be replaced are located within homologous cassettes, which allow gene conversion to proceed.
The sex change operation is initiated by a DS break at a special site in the expressed cassette. This break and other recombination control functions target the gene conversion event so mating type changes with high probability. Interestingly, the DS break mechanisms in budding yeast and fission yeast are different. Budding yeast use a typical endonuclease called HO or SceI. But fission yeast use a modified transposase protein, normally associated with the "illegitimate" process of transposition. Thus, we know that this purposeful specialization of "legitimate" recombination has undergone at least two completely independent parallel evolutionary steps.
A somewhat different use of gene conversion between silent and expressed cassettes takes place in numerous disease microbes (pathogens), both bacteria and eukaryotes. These pathogens use gene conversion to alter the structure of their surface proteins to avoid recognition by the host immune system ("antigenic variation").
In the best-studied cases, the bacterial Lyme disease spirochaete Borrelia, and the sleeping sickness protist Trypanosoma brucei, the genome sequence evidence for cassette recombination is strong, but the process is not as well understood as the yeast mating-type switches. The reason is that rather than two silent and one expressed cassette, as in the yeasts, these pathogens use dozens or hundreds of cassettes to keep ahead of the immune system.
"Legitimate recombination" was assumed to be reasonably uniform in the early days of genetics. That was the basis of constructing genetic maps. We now know homologous recombination can be used "illegitimately" (i.e. targeted either positively or negatively). I think the molecular studies are remarkable in uncovering a striking variety of ways cells have adapted homologous recombination for diverse purposes. As the recent mouse paper shows, we have only begun to scratch the surface of what promises to be a rich vein of cellular inventiveness.
REFERENCE
Bukhari, A. I., J.A. Shapiro, and S. L. Adhya (Eds.) (1977). DNA insertion elements, plasmids and episomes Cold Spring Harbor, New York, Cold Spring Harbor Press.
The following is a summary of how I understand what you are saying about natural genetic engineering and how this blog fits in. Conventional evolutionary theory states that all mutations are random in the sense that they are not biased toward a favorable outcome for the organism in question. The assertion underlying NGE is that cells have the capability to produce mutations which are in fact biased toward a 'favorable' outcome. Cells have a broad range to 'tools' which they can use to perform their NGE operations.
'Legitimate recombination' as customarily understood is not a NGE event because the location of the double strand break involved in the recombination is not targeted. However, the SP011 endonuclease can be used by the cell to cleave preferred genetic sequences: the cell, making use of this endonuclease, is thus able to perform NGE events. Additionally, a 'mouse protein' has been found which can bind to 'genome expression signals' and prevent homologous recombination breaks from occurring at these critical points.
Thus, among the many tools available to cells in their performance of NGE are proteins which can be used to target the double strand breaks involved in recombination events and proteins which will protect important sequences from breaks.
Your critical comments are welcome.
Thanks for trying to reduce this blog to the essentials. I hope the rewrite I just posted will make all this clearer.
Permit me to correct one basic misperception.
Natural genetic engineering refers to cell processes that repair, restructure or change the genome. The name comes from recognizing that these cell operations involve cutting and splicing DNA and performing other tasks associated with human genetic engineering. This is independent of biological utility. NGE as a process can be neutral, harmful or beneficial.
Natural genetic engineering is inherently non-random and, as a complex biochemical process, is subject to cell control. Both the non-randomness and the control provide opportunities for cells to take advantage of natural genetic engineering to produce useful genome innovations. The DNA sequence records shows this has happened many thousands of times in the course of evolution.
The Spo11 and other nucleases that target homologous recombination (a particular kind of natural genetic engineering) illustrate specific ways that cell control directs that process towards adaptive utility. In the case of the protective mouse protein, cell control prevents accumulated adaptations being disrupted by recombination at Spo11 sites (i.e. by NGE).
Like human engineering, natural genetic engineering employs a toolbox of mechanisms for generating novelty. Whether that novelty is useful depends on the control process that picks and chooses when and where to use which tools. Our current scientific challenge is figuring out how that control process has operated so effectively in the course of evolution.
Sorry, off topic. Unfortunately IMHO, your newer articles are still way too complex for the general public to grasp and the problem is that they are far less knowledgeable about evolution.
Sadly, after considering the retention of inconsequential information, the average person remembers being taught that Darwin's evolution is accidental mutations and Natural Selectingsomething. Then there is Darwin’s Tree of life. If they were really paying attention in class, they can recall Finches beaks, Moths changing colors, fish became reptiles, warm little ponds, and Millers experiments.
If they are a Creationist, they have also learned about Piltdown man, Heckels embryos, no fossil records, micro versus macro evolution, and that Darwin was an Atheist.
That's about it! They more than likely have never heard about “NGE”, “HGT,” “Hybridization,” “Symbiogenesis,” or “Epigenetics.” and would probably slide into a coma if the person trying to educate them is communicating to them at the level of a 3rd year Biology student.
So keep it VERY simple and forget about "the “John Kwoks” of the world. For every one “John Kwok” there is 100,000 potential average readers who need to learn from you! However, they should not have to be first versed in the Latin and Greek languages and have a science degree in order to grasp your theories!
Dr. Shapiro, you currently have arguably the most powerful message from science to the general public, but it is worthless if it is not understandable. Your detractors know this…
I would suggest using an analogy but can already foresee the analogy becoming the focus rather than the science. So all I can suggest is perhaps a summation that would include the point that is being made, and perhaps even coin a phrase and give it a name like 'cells with intellects', or something like that :-)
Having really smart people around like John Kwoks to challenge assertions is a valuable asset, not a negative. Lets not ignore arguments and just listen to the choir so to speak.
And lastly. I thought that Darwin was a Methodist minister, and don't remember hearing that he gave up his frock, am I wrong on that ?
You're always true to your name.
As you can see from the response to Philip, I'm working on the communication problem. I'm doing another go at explaining why recombination is not random and how cells make use of that.
Can I count on you to let me know how successful I have been?
Not off topic by any means. This kind of constructive criticism is very welcome.
My challenge is both to educate the public about what is novel in evolution thinking and to show that the new ideas have solid science behind them. I'm aware that often I err too much towards the latter.
I will take your admonitions to heart as I think about the next posting.
Dr. Shapiro, with all due respect, why bother dwelling on the minutia when you have not YET clearly established to the Huff readership that your theories in general are any different than what was pounded into their heads in high school? Only your detractors are demanding MORE "Solid Science"
In fact, nothing on the cover of your book "Evolution: A View from the 21st Century" indicates that its not just more of the same stuff they learned in high school, and quite frankly they ultimately rejected, so why buy it? At least that was my initial impression.
Interesting, your articles give that same impression too because not one of your article titles or their content for that matter, clearly communicates to the layperson that you are any different.
So IMHO, not only do you need to simplify, you need to make it compelling and dramatically clear that your views on evolution are completely different than what was pounded into their heads in high school.
Heck, Pretend If you had an opportunity to contribute to a biology textbook that was required reading for high school biology classes, that express all your different views on evolution. How would you communicate it all in a very very very simple way?
Because who knows, if you figure it out, you might just get that opportunity...
Remember KISS