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Sure, Some Prions Can Cause Diseases, but Others Are Turning out to Be Beneficial

Sure, Some Prions Can Cause Diseases, but Others Are Turning out to Be Beneficial

AlrL Si ve ining Sure, some prions can cause , but others are turning out to be beneficial.

by Richard Saltus illustration by Deth P. Sun

22 hhmi bulletin | May 2o1o

Evn e tHE worstgang of rogues Research at the Massachusetts Institute of Technology. “Prions may reveal surprising qualities that cast them in a more favorable are a really deeply rooted part of normal biology.” light. In fact, evidence is mounting that a class of called She developed this silver-lining view of prions back when prions—despite the fact that their best-known member causes a most scientists saw nothing but their destructive side. In a review rare, deadly -wasting scourge in humans—can also be good written in 1997, Lindquist wrote: “My contention is that and citizens in the of a . mammalian prions are not oddities in a biological freak show, but In 1982, Stanley Prusiner, a biochemist at the University of actors in a larger production now playing in a theater near you.” California, San Francisco (UCSF), isolated the first prion as That prediction is being borne out by a stream of discoveries the cause of lethal in . In 1997, he won a Nobel from her Whitehead laboratory and others in the United States Prize for the achievement and for characterizing a mechanism and abroad. “The real excitement now is to determine how wide- for ­ aggregation and self-perpetuation, or as the Nobel spread this biology is,” Lindquist says. committee wrote, “for his discovery of prions, a new biological principle of .” The good guys In the intervening years, a variety of proteins with primi- The first hint that prions might be advantageous in multicellular­ tive self-sustaining properties have been found in yeast, fungi came in 2003 in a series of studies in the giant marine and , snails, flies, turtles, frogs, birds, mice, and other snail Aplysia californica. A major question in brain research is , including , sheep, deer, , and people. The how are stored. Research in Aplysia had shown that functions of these prions are far more diverse and complex than memories are stored at specific nerve synapses that undergo long- anyone imagined. term strengthening that lasts as long as the lasts. In the Prions are proteins that have converted from a normal config- first of two papers published in Cell in 2003, HHMI investiga- uration to a “misfolded,” self-perpetuating form that reproduces tor and neuroscientist Eric Kandel at Columbia University, and even though it lacks a genetic blueprint like DNA or RNA. Like his former postdoc, Kausik Si, now at the Stowers Institute for one bad apple spoiling the barrel, the prion sets off a cascade, Medical Research, found that the long-term maintenance of converting other proteins of the same kind from which it was this process at nerve synapses requires continuous production formed into prions as well. of prote­ ins, which is regulated by a protein called CPEB. To be sure, some prions are nothing but bad news. That first But how did CPEB keep this process going? Si noticed that one, termed PrPSc by Prusiner, forms toxic , abnormal one end of CPEB resembles the prion found in yeast proteins that aggregate to form tough, fibrous deposits in cells. prions. He suggested that the protein could convert to a self-­ Amyloids spread through the brain and spinal cord, decimating perpetuating form that was distinctively prion-like. He and nerve cells in and humans. Kandel wondered if, when stimulated repeatedly (as in learning), A string of recent findings, however, shows that some prions can the CPEB in synapses could become a self-sustaining protein serve beneficial functions—among them: helping maintain long- that spurs the ongoing of messenger RNA (mRNA) term memories in snails, mice, and fruit flies; fast-forwarding into memory. in yeast to equip them with survival traits; aiding syn- “In principle, this could be how you remember things for the thesis of the pigment melanin in mammals; forming biofilms that rest of your life,” says Kandel. give adhesive properties to bacteria; and storing hormones inside To test this idea Kandel and Si joined forces with Lindquist. endocrine cells. In the second 2003 Cell paper, they observed that CPEB “The prions are just a minor idiosyncrasy,” says HHMI proteins from the Aplysia, when inserted into yeast, formed self-­ investigator , a leading researcher on protein perpetuating units. In a follow-up paper in Cell in February 2010, folding and prions at the Whitehead Institute for Biomedical Si and Kandel showed the same in Aplysia’s own sensory ­:

24 hhmi bulletin | May 2o1o Lenny Gonzalez that had a beneficial effect in allowing cells to try out genetic variation hiddenintheir ,”genetic Lindquist says. out try to cells allowing in effect beneficial a had that an essentialroleinthemaintenance ofyeastprions. plays Hsp104 that observed others and She proteins. aggregated 1998 a dissolving by temperature in in changes to adapt yeast helps showed paper, she which, a Hsp104, on protein, working was “heat-shock” She observations. landmark his published self-replicating andformsfibrousamyloids, justasinmammals. is form PSI+ The psi–. and version—PSI+ prion a and normal a between forth and back switch can as known protein in a normal form and a misfolded prion form. A case in point, the Institutes of Health reported that certain yeast proteins could exist tial benefits of some prions. In 1994, Reed Wickner of the National ­S also existsinhumans. of homolog prion-like of role ­features the probe to system model the using is and a memory. forms that is strengthening form synaptic the prion maintaining the for essential and prion self-sustaining a like acts CPEB accharomyces cerevisiae “Later, my lab reported that PSI+ was an ‘evolvability factor’ factor’ ‘evolvability an was PSI+ that reported lab my “Later, Wickner that time the around field the entered Lindquist yeast fast-growing the in been have studies prion Most the on working is Si in learning and memory. Kandel’s lab group has found a Aplysia and fly CPEB in mice. A homolog of CPEB of homolog A in mice. CPEB fly and , which yielded the first clues to the poten- Aplysia Aplysia CPEB homolog in the fruit fly fly fruit the in homolog CPEB prion phenomenonisanalternate evolutionarypathway. the that argument convincing a building with Lindquist credits who Switzerland, in Zurich of Hospital University the at expert prion a Aguzzi, way,”Adriano non-genetic says a in information have evolvedthroughtheselectivepressureofstress. stress, andchangesincarbonsources. oxidative concentration, salt as such variables environmental to adapt yeast the helps potentially switching prion can by selected that be phenotypes new of collection The states. prion have that proteins 19 uncovered and genome yeast the surveyed had can form beneficialprions. Weissman that someproteins of timesuggests to Jonathan conserved over longperiods Evidence that prionshave been o ncie t esr ta sm o te el srie under survive cells the of some that ensure to inactive, to active or active, to inactive from switch will cells yeast logged water- the in Various prions environment. different drastically a in now is yeast the puddle, a into and vine the from falls yeast more numbers onaroulettewheel.” on money put who gamblers prions—“like become and misfold The more stress the yeast is under, the more likely its proteins will “Westrategy,”speak. ‘bet-hedging’ a as this of explains. think she to so waters, the test to silent previously on sion—turning conver- the make cells of number small a Just prions. to colony whole the switch doesn’t the Lindquist, says ditions, and couldhelptheorganism toevolvemorequickly.” beneficial potentially are that states biological new immediate provides this that think we and cell, the in expression of pattern the change “They explains. Lindquist switched,” is tion ­hundreds ofthousandsyears. for microorganisms in conserved been have they shown, has he as because, beneficial,”—especially are that prions form can’t proteins other that mean doesn’t “that toxic, certainly almost is PrPSc the while that, agrees Lindquist.He with collaboration in also and independently prion PSI+ the of functions survival ied some donot. w ater. Some of those activation switches help the yeast, but but yeast, the help switches activation those of Some ater. “I think the prion principle is a wonderful way to distribute distribute to way wonderful a is principle prion the think “I may prions that suggestion Lindquist’s reinforce results The For example, Lindquist explains, if a grape dusted with with dusted grape a if explains, Lindquist example, For con- changing with confronted suddenly is yeast the When func- their state, prion the into switch proteins the “When L Jonathan Weissman, an HHMI investigator at UCSF, has stud- indquist and colleagues reported in in reported colleagues and indquist Cell Cell May 2o1o May in 2009 that they they that 2009 in

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bulletin ­ 25 Susan Lindquist, Eric Kandel, and colleagues have ­collaborated to show that proteins involved in normal cell processes can convert to a self-perpetuating, prion-like form to maintain memory, for example.

A killer introduction The 1982 discovery of prions by Stanley Prusiner, a biochemist at UCSF, was a stunning answer to a longstanding and stubborn problem: what was the mysterious agent responsible for trans- missible spongiform (TSEs)—progressive, incurable, and lethal diseases that destroy nerve cells and leave a sponge-like trail of destruction? The earliest known TSE was scrapie, an affliction of sheep. Other TSEs now known to be prion diseases are bovine spongi- form (BSE, or mad cow disease) and some very rare but lethal neurodegenerative diseases in humans, including Creutzfeldt–Jakob disease (CJD), variant CJD, , and familial fatal . These diseases have incubation periods measured in years. The BSE epidemic of the 1980s and early 1990s killed 170,000 head of cattle and led to the slaughter of more than If for any reason the protein fails to fold correctly, it may not work 4 million cows, mostly in England, before it subsided. During this at all, or its function may be different from what was specified. epidemic, a form of BSE called variant CJD spread to humans PrPSc, the scrapie prion isolated by Prusiner, is a misfolded who ate meat products from the infected herds. Mad cow disease form of a naturally occurring cell-membrane protein, PrP, which killed about 200 people. is expressed in nerve and elsewhere in healthy people and Scientists had determined that the agent carrying scrapie was many animals. very small and extremely hardy: it couldn’t be inactivated by heat, ultraviolet radiation, or denaturing, which would destroy Reason for being any genetic material used in reproduction. Researchers have spent many years in a frustrating hunt for the Prusiner reported that the cause of scrapie was a novel infec- function of the normal PrP protein. Surely this protein must have tious particle, which he dubbed a “prion,” consisting solely of some other reason for being than to form lethal prions. Studies misfolded proteins, devoid of genetic material. This was hard showed that mice in which the PrP protein was “knocked out” to swallow for many scientists, since even the smallest bacte- were resistant to infection with the misfolded PrPSc prions. ria and have some genetically encoded instructions Otherwise,­ lacking the PrP protein seemed to have little effect. for replication. A piece of the puzzle seems to have fallen into place. Aguzzi For years afterward, some skeptics rejected the “protein-only” and other scientists reported in January 2010 in Nature Neuro- model of prions, arguing that they must contain some genetic science that the protein helps maintain the sheaths that material that had escaped detection. A strong refutation of that surround and protect neurons in the peripheral nervous system. view came in 2000 when Weissman at UCSF reported that he In mice engineered to lack PrP, peripheral nerves suffered pro- had created synthetic prions in a test tube directly from a pure gressive damage as a result of demyelination. Aguzzi said in an yeast protein, Sup35. interview in the journal that he suspects PrP plays a similar role To understand what makes a prion, recall that cells manufac- in higher mammals. ture proteins by assembling chains of amino acids according to a The finding may also bear on another longstanding enigma: “recipe” contained in a specific gene. Then the protein folds into a are prion diseases caused by a “gain-of-function” process—the mis-

three-dimensional configuration like a complex piece of origami. folded protein itself damages nerve cells—or a “loss-of-function”­ Lindquist: Cheryl Senter / AP, ©HHMI Kandel: Matthew Septimus

26 hhmi bulletin | May 2o1o change, in which conversion of the normal protein to prions robs a prion determines its configuration and how the resulting struc- the nerves of something they need to stay healthy? tures differ at the atomic level. Outside the nervous system, another hint of PrP’s normal func- HHMI investigator David Eisenberg, a spe- tion came in a 2006 report from the Lindquist lab. The scientists cialist at the University of California, Los Angeles, uses various found that expression of the protein in stem cells is necessary for types of x-ray crystallography techniques to study the structure of the self-renewal of blood-manufacturing tissues in . the proteins produced by prions. The study showed that all long-term hematopoietic stem cells In 2005, Eisenberg showed that when a protein converts to a express PrP on their surfaces and that blood-forming tissues lacking prion, it polymerizes into an aggregate made up of tightly packed PrP in stem cells exhibited increased sensitivity to cell depletion. layers known as beta sheets (as opposed to the coiled alpha heli- ces that dominate in the normal protein structure). The firmly Structure as blueprint bound beta sheets, held together by an interlocking of their HHMI scientists have begun to decipher another prion riddle— side chains that Eisenberg has termed a “steric zipper,” give the the existence of distinct “strains” of prions that produce different prion its stable, tough properties. In fact, the sheets are so closely phenotypes. For example, the PrPSc prion causes several distinct packed that they exclude water, making prions insoluble. neurological diseases in animals and humans. Each disease is In a 2009 paper in Nature Structural & , slightly different in the length of its , the typical Eisenberg proposed an explanation of how a single protein gives symptoms, and the areas of the brain that are damaged. rise to varying shapes of amyloids that specify different strains. “This was one of the most intriguing and challenging questions,” Instead of DNA alterations, as in living organisms, prion strains explains Weissman. In viruses or bacteria, strain differences are speci- are specified by structural changes that are sufficiently stable to fied by instructions in their . If prions lacked any genetic perpetuate the strain identity in successive prions—and when material at all, where were the blueprints that determine strains? they jump from cell to cell and to animal. Weissman carried out a series of experiments demonstrating In one type of strain-determining mechanism, the same seg- that prions could propagate as distinct strains, each specified by ment of a protein’s sequence can specify different different arrangements of atoms in the protein’s structure. The “packing” arrangements of the beta sheets. In an alternative structural configuration of a prion strain was the blueprint for mechanism, distinctive beta sheets are produced by different making more copies—no DNA required. ­segments of the protein. Using the powerful yeast system, Weissman and colleagues “Our hypothesis is that the differences in packing produce created synthetic prions with different configurations that gener- diverse amyloid fibrils, and these fibers cause different disease ated phenotypically diverse strains. In another experiment, they types,” says Eisenberg. analyzed two distinct strains of the yeast protein Sup35, one of In fact, these variations that Eisenberg is finding at the most which was strongly infectious and the other weakly infectious. fundamental, atomic level may come full circle to explain the The analysis required a special application of nuclear magnetic array of functions—some harmful, some helpful—found in resonance spectroscopy, which enabled him to identify structural ­prions ranging from yeast to humans. differences at the atomic level underlying these ­different pheno- Meanwhile, he and other scientists, including Si, Kandel, types. The results, published in Nature in 2007, confirmed that and Lindquist, are searching for evidence of the positive side the same protein can misfold into dramatically different prion of prions. conformations—which is why the phenotypes they produce can If that search is fruitful, Si has a radical proposal: “Prions have vary so significantly. been so tightly linked to the diseases that if we find more of these Some of the newest prion work takes a deeper look at multiple positive functions, I think eventually we might have to come up strains. The goal is to figure out how the amino acid sequence of with a new name for them.” W

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