Molecular machine may lead to new drugs to combat human diseases

Purdue University ^ | February 18, 2005 | Susan A. Steeves

[Michael_Michaelangelo]

WEST LAFAYETTE, Ind. – The crystallized form of a molecular machine that can cut and paste genetic material is revealing possible new paths for treating diseases such as some forms of cancer and opportunistic infections that plague HIV patients.

Purdue University researchers froze one of these molecular machines, which are chemical complexes known as a Group I intron, at mid-point in its work cycle. When frozen, crystallized introns reveal their structure and the sites at which they bind with various molecules to cause biochemical reactions. Scientists can use this knowledge to manipulate the intron to splice out malfunctioning genes, said Barbara Golden, associate professor of biochemistry. Normal genes then can take over without actually changing the genetic code.

The results of the Purdue study are published in the January issue of the journal Nature Structural and Molecular Biology.

"In terms of human health, Group I introns are interesting because they cause their own removal and also splice the ends of the surrounding RNA together, forming a functional gene," Golden said. "We can design introns and re-engineer them so they will do this to RNA in which we're interested."

Once thought of as genetic junk, introns are bits of DNA that can activate their own removal from RNA, which translates DNA's directions for gene behavior. Introns then splice the RNA back together. Scientists are just learning whether many DNA sequences previously believed to have no function actually may play specialized roles in cell behavior.

[PureSolace]

This is good news.... but also we have a responsibility to make sure that thie technology is not misused (especially by would be bio terrorists. If we can make nano strains that go around changing things for the good, imagine the horrors of being able to destroy with the same technology. Stay Safe.

[Redcloak]

Let's just hope that they don't look like these...

[jennyp]

Really, now? It seems to me the argument was that, necessarily, "junk" was a basic component of a "random" process. In fact, most of DNA should be a complete wasteland of unused and "decaying" parts.

But junk DNA would be analogous to an unused organ. Since there's some nonzero cost to keeping & reproducing an unused DNA sequence, any deletion of a truly junk sequence should be slightly favored over time. Or maybe the energy cost of any single unused stretch is negligible, so its deletion wouldn't get selected out. But regardless, there's more to evolution than just saying "randomness happens" and leaving it at that.

[jennyp]

This is great news. Now that we don't look upon these introns as genetic "junk" (where did that term originate, anyway?), maybe we'll be able to combat some diseases more effectively.

Ahem. The harnessing of the intron's splicing ability to excise out bad RNAs is more evidence that the original life was RNA-based. (Or at least in only makes sense in light of the RNA-world theory):

Introns' unique capability of cutting and pasting apparently has been conserved since life evolved.

"It's thought that RNA, or a molecule related to RNA, possibly were the first biomolecules, because they are capable of both performing work and carrying around their own genetic code," Golden said.

LOL!

Do you realize, Michael (and Andrew), that the only thing here that's new is that they're harnessing the intron's ability to splice itself out of the RNA sequence. This ability has been known for like 25 years.

[Elsie]

To your room, and no supper for YOU, either!

[Elsie]

No supper for YOU, too!!!


You KNOW that ALL websites that have even a HINT of anti-E bias have been thoroughly, soundly, repeatedly, scientifically and logically proven to be tubs of so much bull hocky by our learned associates.

Only a troglodyte would find the slightest bit of humor (hah!) in them.

[Elsie]

(Think new Budwiser ads....)

[Elsie]

WEST LAFAYETTE, Ind. – The crystallized form of a molecular machine that can cut and paste genetic material is revealing possible new paths for treating diseases such as some forms of cancer and opportunistic infections that plague HIV patients.

 

 

 

 

Ok...............

 

 

 

[<1/1,000,000th%]

Prior to the discovery that "junk" DNA had a purpose(IOW it had no use), the situation made sense in light of evolution. Now that the "junk" DNA has been discovered to have a purpose(IOW it has a use), the situation makes sense in light of evolution. LOL. Talk about falsifiability.

This has always been a creationist/ID strawman. Just like "evolution can't explain the eye so evolution is false". This has been repeated in these threads forever. I'm sure you were in on some of these threads AndrewC.

Speculate all you want, but junk DNA is still junk DNA. Until someone finds out what it does and why it isn't conserved - and someone might - it's still junk.

[AndrewC]

This has always been a creationist/ID strawman.

Well, your attempted strawman won't stand. It was not the creationist/ID'er that named the DNA as junk. It was named junk, by those that require junk in the justification of a certain theory.

[AndrewC]

Do you realize, Michael (and Andrew), that the only thing here that's new is that they're harnessing the intron's ability to splice itself out of the RNA sequence. This ability has been known for like 25 years.

Well, I'm not sure of your take on it, especially in light of your previous arguments lumping introns with junk.

Are Introns In-series Error-detecting Sequences?

In eukaryotes the sequence of DNA bases coding for a protein is often found to be interrupted by sequences of bases (introns) which show no obvious relationship to the coding sequence (Gilbert, 1978). Speculation on the possible role of introns has included the view that they are examples of "junk" or "selfish" DNA, which does not contribute positively to cell function (Doolittle & Sapienza, 1980; Orgel & Crick, 1980). However, the notion of message sequences interrupted by non-message sequences is quite familiar to those working on noise affecting signal transmission in electrical systems. In these systems the non-message sequences have an error-checking function and permit the receiver to detect and correct errors in the message sequence (Hamming, 1980). Some principles which may guide investigations of a possible error-checking role for introns are outlined in this paper.

[Captain Beyond]

bump

[jennyp]

That's an interesting page you found. It raises some good questions about introns' function.

But surely you must have noticed the (short) summaries of the history of thought surrounding introns' functions. Here's a part of his summary from the top of the page:

If introns could be dispensed with in bacteria, then perhaps they had no function. Alternatively, whatever function introns had, either was not necessary in bacteria, or might be achieved in other ways by bacteria. Since members of many bacterial species appeared to be under intense pressure to streamline their genomes to facilitate rapid replication, if it were possible they would have dispensed with any preexisting introns and/or would have been reluctant to acquire them. On the other hand, if introns played a role and/or did not present too great a selective burden, eukaryotes would have tended to retain preexisting introns, or could have acquired them.

Knowing the function of introns seemed critical for sorting out these issues. There were many ingenious suggestions. Some thought introns were just another example of the apparently non-utile "junk" DNA which littered the DNA of many eukaryotes. However, some principles to guide investigation of a possible error-checking role were presented (Forsdyke 1981), and there is now growing evidence that introns play such a role (Forsdyke 1995a,b), although the mechanism may be somewhat different to that originally proposed (Liebovitch et al. 1996. Biophys. J. 71, 1539-1544). It appears that the order of bases in nucleic acids might have been under evolutionary pressure to develop the potential to form stem-loop structures which would facilitate "in-series" or "in-parallel" error-correction by recombination.

Although the genetic code is degenerate (more than one codon per amino acid so that there is some flexibility as to which base occupies a particular position), there is still room for conflict between the "desires" of a sequence to encode both a protein (or non-messenger RNA) and stem-loop potential. The conflict would be particularly apparent in the case of genes under very strong positive phenotypic (Darwinian ) selection, as in the case of genes affected by "arms races" with predators or prey.

For example, [snakes with their venom vs. the rodent's immunity to the venom] constitutes an "arms race", and influences particular genes. The part of the venom protein which is important for toxicity is required to change so very rapidly in response to this strong phenotypic pressure from the environment, that the corresponding gene can no longer afford the "luxury" of trying to encode both the best protein and the best stem-loops. So the stem-loop role is left to the introns. Here, paradoxically, sequence conservation is high, whereas in the exons, sequence conservation is low (Forsdyke 1995b). Similar pressures may be acting of the peptide binding regions of the genes encoding major histocompatibility antigens (Forsdyke 1996b).

Subsequent to the publication of the latter papers, another "player" in the conflict between protein-encoding potential and stem-loop potential emerged. Most mRNAs are "purine-loaded" in the loop regions of stem-loop structures (reviewed in Forsdyke & Mortimer, 2000). The selection pressure for this appears to operate primarily at the cytoplasmic level. Consequently, the purine-loading may not optimally serve the postulated genomic role of stem-loops. There may be a conflict between "AG-pressure" (the pressure to purine-load) and stem-loop pressure. To resolve this, stem-loop potential would be moved to a region where AG-pressure does not operate, the introns.

Now, I don't fully understand what he's saying here, but it seems that several types of RNAs have to be able to loop back on themselves like a sewing needle, called a "stem loop". It's likely a throwback to the days when RNA was both the cell's information-carrier and metabolic workhorse. This dual job-description still holds somewhat (otherwise the physical conformation of the RNA shouldn't be an issue). Anyway, it's obvious he's describing a proposed benefit to having introns, and discussing it in terms of Darwinian selection forces. Not only that, but his references for these evolution-inspired hypotheses go back as far as 1981. As Larry Elder would say: "Hmmm!"

Further down, look at this

In 1985 when considering gene duplication, Russell F. Doolittle pondered (Trends in Biochem. Sci. June):

"I still favor the notion that the principal selective value of introns concerns genetic maintenance, as was suggested by many when introns were first discovered. It is the preventing of mismatches of duplicated genes during meiosis and mitosis that is so crucial to eukaryotes. The free and easy nucleotide substitution that occurs in introns should serve as a buffer against [chromosome] mispairing while allowing the advantages of sets of similar gene products. Sets of multiple gene products allow adaptation for regulation of different parts of the life cycle or for different tissues."

Doolittle's focus here is on the prevention of pairing between the sequences of duplicate genes. By preventing pairing, potential recombination events would be discouraged. Since duplicate genes have similar sequences, and recombination can occur when sequences are similar, then the introduction of introns that are more able to accept mutations (i.e. to diversity), would serve to preserve the duplicate genes (i.e. prevent them blending by recombination). This theme was extended to involve differences in GC% and isochores by Matsuo and coworkers....

So here we have a prominent evolutionary biologist saying that right from the start, biologists were using evolution to deduce what the role of introns must be. Not only that, but Doolittle's hypothesis is that they help preserve newly-duplicated genes, the very source of increased complexity throughout macroevolution! HMMMMM....

I'm beginning to think that this "evolution blinded biologists to the functionality of 'junk DNA'" talking point is pure strawman.

(Pinging some others who might find this historical context interesting.)

[AndrewC]

But surely you must have noticed the (short) summaries of the history of thought surrounding introns' functions.

Of course I did. That is why I posted it. Now, certainly, you must realize that it probably never was "junk" as you have previously argued. That argument , that it was "junk" had a reason, and that reason was in support of a certain theory. That it is not "junk" is, therefore, in contradiction to that certain theory.(that is, if the theory is to be credibly falsifiable as it is constantly alleged)

[AndrewC]

May I remind you of Dr. James Shapiro

LINEs are master genetic engineers, and it has been argued that they are the major force in structuring mammalian genomes (44). Often LINE transcription does not terminate at its polyA tail but reads through into adjacent DNA; upon reverse transcription and integration into an intron, this adjacent sequence material can form part of a new regulatory region or a coding exon. In fact, LINE-mediated exon shuffling to create new multidomain proteins has been experimentally demonstrated (45). In addition, LINE element activities can reverse transcribe and insert cellular mRNAs into the genome, creating extra intron-free copies of a coding sequence. This process is the source of "processed pseudogenes" in the genome, and apparently it also has played a major role in the amplification of olfactory receptor proteins that are major adaptive inventions of mammals (46).

[Ichneumon]

The truth is odds over 1 in 10 to the 50th power are considered "impossible" by statisticians.

The odds of shuffling a deck of cards and getting a particular sequence is actually far longer odds than that. Is shuffling a deck of cards "considered 'impossible' by statisticians"? Or are you just really confused about this "math" thing you heard about in passing? Obviously, you've made an error in your so-called "reasoning" somewhere.

Furthermore, you're vastly confused about both the source and the application of the "1 in 10 to the 50th power" rule of thumb. If you care to, you know, actually learn something for change, read on -- here's a reply I made to yet another clueless person making the same false claim:

So the odds against this organelle forming are are very much less than the inverse of 1x10 to the 100th power.

Correct even after your errors have been corrected. But again, one must realize that these are only "the odds against this organelle forming" *totally at random all at once" by sheer chance of jostling amino acids in a bucket. It is *not* the odds against the organelle forming by evolutionary processes.

Physicists call anything less likely than 1x10 to the 50th power "impossible".

Funny you should mention that... First, "physicists" don't say that, since events less likely than that easily occur. For example, shuffle a deck of cards, then spread the deck face-up on a tabletop. Congratulations, the odds of that particular arrangement of cards occurring as a result of a shuffle is less than 1.24x10^-68, which is far less than 1x10^-50 -- it's a miracle!

Second, even rare events chosen a priori occur easily enough when the number of trials is large enough. For example an atomic state which occurs in less than 1x10^-50 atoms is a near certainty to occur in the Earth alone, which contains far more than 1x10⁵⁰ atoms.

So the "law" you mention is incorrect as stated.

But what's really funny about you mentioning it is that it's an informal rule of thumb (for *human* watchable events, not meant to be applied universally), originated by Emil Borel in a couple of books he wrote in 1943 and 1950 to popularize science. It's sometimes affectionately known as "Borel's Law". And ironically, Borel himself wrote on the topic of biological probability calculations:

In conclusion, I feel it is necessary to say a few words regarding a question that does not really come within the scope of this book, but that certain readers might nevertheless reproach me for having entirely neglected. I mean the problem of the appearance of life on our planet (and eventually on other planets in the universe) and the probability that this appearance may have been due to chance. If this problem seems to me to lie outside our subject, this is because the probability in question is too complex for us to be able to calculate its order of magnitude. It is on this point that I wish to make several explanatory comments.

When we calculated the probability of reproducing by mere chance a work of literature, in one or more volumes, we certainly observed that, if this work was printed, it must have emanated from a human brain. Now the complexity of that brain must therefore have been even richer than the particular work to which it gave birth. Is it not possible to infer that the probability that this brain may have been produced by the blind forces of chance is even slighter than the probability of the typewriting miracle?

It is obviously the same as if we asked ourselves whether we could know if it was possible actually to create a human being by combining at random a certain number of simple bodies. But this is not the way that the problem of the origin of life presents itself: it is generally held that living beings are the result of a slow process of evolution, beginning with elementary organisms, and that this process of evolution involves certain properties of living matter that prevent us from asserting that the process was accomplished in accordance with the laws of chance.

Moreover, certain of these properties of living matter also belong to inanimate matter, when it takes certain forms, such as that of crystals. It does not seem possible to apply the laws of probability calculus to the phenomenon of the formation of a crystal in a more or less supersaturated solution. At least, it would not be possible to treat this as a problem of probability without taking account of certain properties of matter, properties that facilitate the formation of crystals and that we are certainly obliged to verify. We ought, it seems to me, to consider it likely that the formation of elementary living organisms, and the evolution of those organisms, are also governed by elementary properties of matter that we do not understand perfectly but whose existence we ought nevertheless admit.

Similar observations could be made regarding possible attempts to apply the probability calculus to cosmogonical problems. In this field, too, it does not seem that the conclusions we have could really be of great assistance.

-- Emil Borel, "Probability and Certainty", p. 124-126

So there.

The Odds of single bacterium forming from "pre-existing soup" have been estimated to be at least 1 in 10 to the 100,000,000,000th power!

Totally at random maybe, sure, but since no one who actually knows anything about biology suggests that it *did* happen that way, you're just being goofy. You're modeling the wrong process, so your "results" say absolutely nothing about the odds of anything in the real world. Nice try.

Would it be too much to ask that you go *learn* something about these topics, so that you can evaluate for yourself whether the twaddle you find on various creationist sites is a complete waste of everyone's time or not before you parrot them endlessly? Spreading misinformation does FreeRepublic no service whatsoever, and only helps to "dumb down" discussions. Leave that to the liberals.

[Ichneumon]

Only a troglodyte would find the slightest bit of humor (hah!) in them.

So you think it's funny to spread misinformation and use it to dishonestly reinforce false bigotry? Fascinating.

[Ichneumon]

[Some confused anti-evolutionist wrote:] LINEs are master genetic engineers, and it has been argued that they are the major force in structuring mammalian genomes (44). Often LINE transcription does not terminate at its polyA tail but reads through into adjacent DNA; upon reverse transcription and integration into an intron, this adjacent sequence material can form part of a new regulatory region or a coding exon. In fact, LINE-mediated exon shuffling to create new multidomain proteins has been experimentally demonstrated (45). In addition, LINE element activities can reverse transcribe and insert cellular mRNAs into the genome, creating extra intron-free copies of a coding sequence. This process is the source of "processed pseudogenes" in the genome, and apparently it also has played a major role in the amplification of olfactory receptor proteins that are major adaptive inventions of mammals (46).

Translation: This kind of junk DNA provides randomness and additional mutations which are useful for evolution. Thanks for providing further support for our position. Feel free to shoot yourself in the foot any time.

[Ichneumon]

[Mr. LLLICHY wrote:] It is worse than that. Chemistry has a habit of producing compounds that are not desired.

Oh no, the dreaded "undesired compound"...

That is the reason specific reagents, conditions, and reaction times are required in chemical syntheses for specific compounds.

Yes, if one wants to produce a PURE batch of a pre-chosen product. This, of course, has absolutely nothing to do with the sort of biology under discussion, which would involve a *mix* of many various compounds. Red herring, anyone? It seems to be spawning season for that variety of fish today.

Now imagine what a chemical "soup" would contain,

Thanks, but I prefer to actually follow the evidence and the laws of chemistry in order to determine that, not just do like the anti-evolutionists who draw "conclusions" based on their limited and biased "imaginations".

Oh look, here comes an "imaginary" conclusion now:

certainly nothing desirable for the formation of polymeric amino acid compounds.

Oh, yes "certainly"... Because your "imagination" produces "certain", undeniable, provable results. Got it.

IOW, you don't even get the soup you need in order to make proteins.

In your "imagination" you don't, anyway.

(Could someone explain to me why the anti-evolutionists seem to rely on their own fantasies so often, instead of actual evidence and experiments and so on? Or is the answer as simple as the fact that if they were wont to actually *learn* about the subject, they would not long remain anti-evolutionists, and would join the 99+% of biologists who know that evolution is strongly supported by the mountains of evidence and countless experiments?)

[Ichneumon]

I'm beginning to think that this "evolution blinded biologists to the functionality of 'junk DNA'" talking point is pure strawman.

But... That would be *so* out of character for both that particular poster, and anti-evolutionists in general.

Oh, wait, no it wouldn't, my mistake.

Jennyp, based on previous experience, I believe you will find yourself having to deal with a storm of red herrings now in response to your post, so be prepared.

Also be prepared to point out that contrary to bone-headed (and unsupported) claims that "it probably never was 'junk'", the fact remains that even though rare cases have been found of specific pieces of "junk DNA" (i.e. non-coding DNA) having some use, only an idiot would leap from that to the conclusion that "it probably never was 'junk'" on the whole, because a) the vast majority of "junk DNA" is non-conserved, a clear indication that it is, indeed, not used in the genome, among many other lines of general evidence supporting the same conclusion (is your correspondent ignorant of these, or just dishonest?), and b) specific tests of "junk DNA" have shown that if it's used at all, the use is extremely rare or subtle, because giant whacking swatches of it can be removed entirely without any kind of obvious harm to the animal.

For example: Megabase deletions of gene deserts result in viable mice. In short, the researchers snipped over 2.3 *million* basepairs of apparently "junk DNA" out of mouse DNA, then produced offspring mice which were entirely missing that DNA. The resulting mice were normal in all respects. As a press release states:

"In these studies, we were looking particularly for sequences that might not be essential," said Eddy Rubin, Director of the JGI, where the work was conducted. "Nonetheless we were surprised, given the magnitude of the information being deleted from the genome, by the complete lack of impact noted. From our results, it would seem that some non-coding sequences may indeed have minimal if any function."

A total of 2.3 million letters of DNA code from the 2.7-billion-base-pair mouse genome were deleted. To do this, embryonic cells were genetically engineered to contain the newly compact mouse genome. Mice were subsequently generated from these stem cells. The research team then compared the resulting mice with the abridged genome to mice with the full-length version. A variety of features were analysed, ranging from viability, growth and longevity to numerous other biochemical and molecular features. Despite the researchers' efforts to detect differences in the mice with the abridged genome, none were found.

Another specific piece of evidence is that the genome of the fugu fish (as well as other fish in the blowfish family) is remarkably "clean" compared to that of other fish (or other vertebrates), even other fish which are rather closely related. It's *missing* most of the DNA that other fish (and vertebrates) have that are collectively known as "junk DNA", and as a result has a genome that is nearly "pure" genes (i.e. coding regions) stripped of most non-coding regions. And the fugu gets along just *fine* without them. How and why its genome got "streamlined" by "cleaning house" of most of its "junk DNA" is a fascinating question which is being looked into, but the fact remains that if this "junk DNA" is all that critical and "actually" used for something after all, on the whole, then how does the fugu do so swimmingly (sorry, bad pun) without it at all?

So I repeat -- there are very good reasons, based on testing and on the evidence, that "junk DNA" on the whole really is "junk". And that doesn't change even if a *few* specific non-coding regions end up being involved in gene expression or whatnot. Finding a few discarded items of value in the city dump doesn't magically change the whole thing into a mountain of pearls.

Finally, you might want to point out that his subsequent "conclusion" falls flat because it is based on a false premise: "That it is not 'junk' is, therefore, in contradiction to that certain theory". Complete twaddle. First, it has in no way been established that it in fact "not junk" on the whole. Evolution does not *require* non-coding regions to be totally useless. Nor does it require that they not be. That doesn't change the fact that even if *some* fraction of "junk DNA" is useful in some manner, *any* significant amount of "junk" in the genome is more in keeping with the expected results of evolutionary processes, than with "intelligent design". Ah, now we glimpse what might be his real motivation for struggling mightily against the conclusion which the evidence actually supports... ("It *must* be useful, it *must* be -- g-d doesn't make junk!)

Unlike his false accusations, scientists actually go where the evidence takes them (as they have in this case).