Simpler does not always mean “easier to understand: ”
Going down in size from our kind of complex cells to prions, thus far, the simplest & strangest biological agents of them all
As the scale of matter that is considered to be alive, or at least, active in living systems and able to reproduce itself, has gotten smaller over time, the newly discovered and ever smaller units have fewer and fewer components.
The questions arises: How small and how simple can they get?
For eukaryotes (that is the kind of cell we’re mostly made of ….as are most animals and many plants) you need a cell membrane or cell wall that contains the cytoplasm, and a variety of specialized organelles within it, most notably a nucleus within that cell, that has its own membrane, and that contains multiple, separate strands of nucleic acids, like DNA or RNA, and usually both.
All these are necessary for the eukaryotic cells to function, through the production and metabolism of proteins, fats, and carbohydrates, and especially are required for these cells to reproduce themselves.
It took us about 200 years after the microscopic discovery of eukaryotic cells to get much of a basic understanding of how they functioned, with the DNA/RNA/ protein synthesis part becoming clear only in the late 1950s.
For prokaryotes (and this includes most bacteria and archaea ) there are few if any organelles, and there really is no nucleus. The bacterial and archaeal cell contains only a single loop of DNA, which can make RNA, and together these nucleic acids make the proteins, lipids and carbohydrates necessary for the unit as a whole to function.
And, surprisingly, this much simpler arrangement still also carries all the DNA information necessary for this simpler organism to reproduce.
We figured how bacteria really work only a little while later than we did the eukaryotes, because it was apparent early on that bacteria, in particular, could cause diseases.
Furthermore, some bacteria, particularly E-coli, turned out to be great tools for understanding genetics and the work of DNA. Their very simplicity made them ideal for experimental purposes. A check of WorldCat discloses literally hundreds of books and dissertations on E. coli even now. (See Glass, 1982; Vaillancourt, 2003, & Zimmer, 2008, cited below by way of example.)
Viruses are even more stripped down than bacteria and archaea. They can be described pretty much as nucleic acids protected by a protein coat. No membranes. No cytoplasm. No organelles. No nucleus. No carbohydrates. Very rarely, some have lipids as a secondary protective coat, but most have none.
The overwhelming majority of viruses then, are just DNA or RNA and their protective protein coat. That coat also enables them latch onto and pierce the membranes of bacteria, archaea, or eukaryotes.
Once inside the cell, viruses hijack the cellular machinery of their unwitting hosts in order to function and reproduce through simply replicating their own DNA or RNA and those proteins coats, instead of what is needed by the cell.
It took only about a decade longer to figure to figure this out, largely because electron microscopy was vastly improved by this time and the need to make anti-viral vaccines and drugs had accelerated research.
And curiously the nature of a disease that infected a then important cash crop, called the Tobacco Mosaic Virus, proved almost as important. TMV had whole books written about it, ( see Scholthof, Shaw & Zaitlain, 1999, cited below by way of example) , and took on a life of its own as a model organism.
In any case, for the bulk of the twentieth century, it was thought that viruses were about as small and simple as biology could get.
But while there were early inklings that there could be something smaller that mattered to biology, it was not really until 1982 that someone could isolate that something smaller and give it a name.
That someone was Stanley Prusiner, and that name was “prion. “ Ultimately this got Prusiner the 1992 Nobel Prize, and prions too, have gotten their own whole books.
Prions are even simpler than viruses. They have no DNA or RNA. They have only misfolded proteins, yet somehow they manage to reproduce themselves.
This would seem to be a kind of magic trick except for the fact that prions seems to be the cause of obscure but invariably fatal human neurological diseases like Creutzfeld-Jacob, as well that of important agricultural diseases like scrapie in sheep and goats and mad cow disease.
This latter obvious affects cows, and sometimes humans who eat the neurological parts of cows (largely portions of their brains, spinal cords, or muscle tissue with extensive innervation.)
Ironically, while these agricultural diseases had been well known but not well understood back into the 1700s, the fact that human infections could be caused by what were later shown by workers like Prusiner to be prions, had actually won the Nobel Prize for another scientist Carleton Gajdusek much earlier, back in 1976.
Gajdusek noted that certain South Sea island cannibals came down with the bizarre and fatal illness of kuru, through the ritualized eating of the brains of deceased relatives who had been previously infected with this mysterious agent we now know as prions.
But many questions remained. How do prions form and reproduce themselves? Are all proteins capable on some level of turning into prions? Do prions turn into something else. Are they involved in other diseases?
While the mad cow disease panic of the late 1990s caused quite an impetus to prion research, perhaps no greater reinforcement has come to pass since the discovery that those misfolded prion proteins are very similar to another disease which seems to involved misfolded proteins: Alzheimer’s.
Alzheimer’s Disease involves , within the brain, tangles of fibrils or sheets of proteins that have today become best known by their structural classification as beta-folded amyloid proteins.
Have we found a simple model system to understand better the conditions that turn proteins into prions?
Just as we have used smaller and simpler biological systems to better understand general biological phenomena, much as we used the bacterium E. coli to study general genetics or TMV to study general virology, it turns out that the simple microorganisms, the yeasts, have an abundance of proteins, some of which seem to have the tendency to become prionogenic.
In other words, they tend to form disordered beta- sheets, that remarkably tend to be passed on between different generations of yeast.
The type of yeast used had a relatively simple form of reproduction, called budding,
In budding, daughter yeast cells grow in interior dents within the parent yeast membrane, and when the daughter compartment gets large enough, it breaks off without damaging the parent yeast cell, and assume an independent existence.
And fortunately for the yeast, and for the researchers who needed a stable, non-infective source of prions and a model system to study their manufacture, these beta-sheets do not seem to harm the yeast, and in fact, have some beneficial effect in terms of the yeast’s own structure.
Over time, a variety of clearly prionogenic proteins ( among those most commonly mentioned are those labeled as Sup35p, Ure2p, and Rnq1p ) have popped up in these yeasts, and yet, few common factors could be detected among them.
Among those few facts was that each of these prionogenic proteins resisted a chemical treatment called denaturing, which, while primarily a lab procedure, is indicative of extra survival capability.
In addition, all these prionogenic proteins had structural sequences that were rich in either glutamines or asparagines.
Building on some earlier pioneering work on genomic and proteomic screening, as well as some studies of protein structures using magnetic resonance imaging, Alberti et al. (2009, cited below) developed a systematic screening procedure for sorting out which yeast proteins are prionogenic, and then analyzed these to find commonalities. Fowler & Kennedy (2009, cited below) provide us with a very helpful summary of how this process worked
Albert et al. used a 3-way screening procedure involving 100 different candidate proteins.
Candidate prionogenic proteins had to show that they formed aggregates in living yeast that were supplied with all the usual protein precursors in culture that would enable them easily to manufacture proteins, (and therefore beta sheets) , in abundance . 69 out of 100 candidates passed this test.
Candidate prionogenic proteins had to form aggregates in relatively protein deprived in-vitro tests. Despite the lack of a healthy protein assembly line in operation, 50 of the 69 remaining candidates passed this test, scavenging enough material to form aggregates in three days.
These successful prionogenic proteins all shared that highly indicative denaturing resistance factor.
Finally candidate prionogenic proteins had to work well with another protein called Hsp104p, which was important to the reproductive budding process, so that enough of the prionogenic proteins reliably transferred into each bud, so as to perpetuate the prions and their resulting beta sheets in succeeding generations of yeast.
In other words, the prions had the capacity to assemble themselves not only in parents but also in their daughters on a continuous basis.
19 candidate prionogenic proteins passed this final test.
What was most surprising about this group of finalists ? The fact that they were resistant to denaturing was reassuring but not the most unexpected finding.
That was that protein sequences rich in asparagines were dramatically more likely to be prionogenic than were those rich in glutamine.
This may seem like a small triumph, but it is a triumph of figuring out what raw materials seem to work best in a model assembly line from which we wish to extrapolate the more complicated and still mysterious beta-sheet amyloid-making processes going on in our aging brains.
Tony Stankus [email protected] Life Sciences Librarian & Professor
University of Arkansas Libraries MULN 223 East
365 North McIlroy Avenue North
Fayetteville AR 72701-4002
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Alberti, A. Halfman, R., King, O., Kapila, A, & Lundquist, S. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell, 137, 146-158.
Bahmanyar, S., Higgins, G.A., Goldgaber, D., Lewis, D.A., Morrison, J.H., Wilson, MC., Shankar, S.K. & Gajdusek, D.C. Localization of amyloid-beta protein messenger RNA in brains from patients with Alzheimer’s Disease. Science, 237 (4810), 77-80.
Chae, Y. K., Cho, K. S., & Chun, W. (2002). A prionogenic peptide derived from Sup35 can force the whole GST fusion protein to show amyloid characteristics. Protein and Peptide Letters, 9(4), 315-321.
Chae, Y. K., Lee, K., & Kim, Y. (2004). NMR studies of the prionogenic peptide derived from Sup35 protein. Protein and Peptide Letters, 11(1), 23-28.
Fowler, D.M. & Kelly, J.W. (2009. Aggregating knowledge about prions and amyloid. Cell, 137, 20-22.
Gajdusek, D. Carleton. (2008). Kuru and its contribution to medicine. Philosophical Transactions of the Royal Society of London B – Biological Sciences, 363 (1510), 3697-3700.
Glass, R.E. (1982). Gene Function: E. Coli and its Heritable Elements. Berkeley, CA: University of California Press.
Klitzman, R. 1998. The trembling mountain: A personal account of kuru, cannibals, and mad cow disease. NY: Plenum Trade Books.
Prusiner, S. B., ed. ((2004). Prion Biology and Diseases. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2004.
Scholthof, K.B.G., Shaw, J.G. & Zaitlin, M. eds. (1999) Tobacco Mosaic Birus: One Hundred Years of Contributions to Virology. St. Paul, MN: American Phytopathological Society Press.
Tanaka, M., & Weissman, J. S. (2006). An efficient protein transformation protocol for introducing prions into yeast. Methods in Enzymology, 412, 185-200.
Vaillancourt, P.E. ed. (2003). E. Coli Gene Expression Protocols. Totawa, NJ: Humana Press, 2003.
Volkov, K. V., Aksenova, A. Y., Soom, M. J., Osipov, K. V., Svitin, A. V., Kurischko, C., et al. (2002). Novel non-Mendelian determinant involved in the control of translation accuracy in Saccharomyces cerevisiae. Genetics, 160(1), 25-36.
Yam, P. (2003). The Patholgical Protein: Mad Cow, Chronic Wasting, & Other Deadly Prion Diseases. NY: Copernicus Books, 2003. (A popularization).
Zimmer, C. (2008). Microcosm: E. Coli And The New Science Of Life. NY: Pantheon Books.
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Keep on posting!| I {{leave|drop|{write|create}} a {comment|leave a response}|drop a {comment|leave a response}|{comment|leave a response}} {each time|when|whenever} I {appreciate|like|especially enjoy} a {post|article} on a {site|{blog|website}|site|website} or {I have|if I have} something to {add|contribute|valuable to contribute} {to the discussion|to the conversation}. {It is|Usually it is|Usually it's|It's} {a result of|triggered by|caused by} the {passion|fire|sincerness} {communicated|displayed} in the {post|article} I {read|looked at|browsed}. And {on|after} this {post|article} SLA Biomedical & Life Sciences Division Blog: Prion proteins: How studies of yeast help us understand the assembly line manufacturing of beta-folding amyloid plaques strongly associated with Alzheimer’s Disease in humans.. 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I {like|wanted} to write a little comment to support you.| I {always|constantly|every time} spent my half an hour to read this {blog|weblog|webpage|website|web site}'s {articles|posts|articles or reviews|content} {everyday|daily|every day|all the time} along with a {cup|mug} of coffee.| I {always|for all time|all the time|constantly|every time} emailed this {blog|weblog|webpage|website|web site} post page to all my {friends|associates|contacts}, {because|since|as|for the reason that} if like to read it {then|after that|next|afterward} my {friends|links|contacts} will too.| My {coder|programmer|developer} is trying to {persuade|convince} me to move to .net from PHP. I have always disliked the idea because of the {expenses|costs}. But he's tryiong none the less. I've been using {Movable-type|WordPress} on {a number of|a variety of|numerous|several|various} websites for about a year and am {nervous|anxious|worried|concerned} about switching to another platform. 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IE {still|nonetheless} is the {marketplace|market} {leader|chief} and {a large|a good|a big|a huge} {part of|section of|component to|portion of|component of|element of} {other folks|folks|other people|people} will {leave out|omit|miss|pass over} your {great|wonderful|fantastic|magnificent|excellent} writing {due to|because of} this problem.| {I'm|I am} not sure where {you are|you're} getting your {info|information}, but {good|great} topic. I needs to spend some time learning {more|much more} or understanding more. Thanks for {great|wonderful|fantastic|magnificent|excellent} {information|info} I was looking for this {information|info} for my mission.| {Hi|Hello}, i think that i saw you visited my {blog|weblog|website|web site|site} {so|thus} i came to “return the favor”.{I am|I'm} {trying to|attempting to} find things to {improve|enhance} my {website|site|web site}!I suppose its ok to use {some of|a few of} your ideas!!\
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