News this Week

Science  05 Apr 2013:
Vol. 340, Issue 6128, pp. 14
  1. Around the World

    1 - New Delhi
    India Denies Cancer Drug Patent
    2 - Ottawa
    Canada Withdraws From U.N. Desertification Treaty
    3 - Graz, Austria
    ESA Eyes Forest-Measuring Space Mission
    4 - Shanghai, China
    New Avian Flu Kills Two

    New Delhi

    India Denies Cancer Drug Patent

    India's Supreme Court this week denied a patent sought 7 years ago by Novartis, the Swiss pharma company, for a crystal (pill) form of its celebrated anticancer drug Glivec (also known as Gleevec).

    Groups pushing for low-cost medicines, such as Doctors Without Borders, cheered, while biotech and pharmaceutical groups warned of a possible chill in new drug development. The immediate impact will be to clear the way for cheap Indian versions of Glivec. According to The Wall Street Journal, the cost of treatment with Novartis's Glivec is about $1900 per month compared with $175 per month for generic drug versions made by Indian companies.

    The key molecule (imatinib) was patented outside India in 1993, but India's patent office—which has not given Novartis a patent on any form of imatinib—rejected the company's request for a patent on the crystalline form in 2006 on the grounds that it wasn't a significant innovation. The Indian Supreme Court upheld that decision.

    Novartis, noting that it provides Glivec free of charge to 95% of patients in India who receive a prescription for it, issued a statement saying that the court's decision "discourages innovative drug discovery essential to advancing medical science."

    Ottawa

    Canada Withdraws From U.N. Desertification Treaty

    CREDIT: ANNA RIDOUT/OXFAM INTERNATIONAL/WIKIMEDIA COMMONS

    Canada's Conservative government announced last week that it is withdrawing from a U.N. convention to combat desertification signed by 194 other nations, fueling critics' concerns that the country is increasingly an outlier on climate change. Green Party leader Elizabeth May decried the move as a sign of the Conservative government's indifference to environmental protection. Prime Minister Stephen Harper said the move was about fiscal prudence, with only 18% of Canada's annual contribution of CAD$350,000 "actually spent on programming" rather than bureaucratic measures, he told Parliament last week during a question period.

    Noting that Canada was one of the first countries to sign onto the 1994 treaty, New Democratic and foreign affairs critic Paul Dewar said its decision to withdraw shows "that they either did not understand this convention, or they're willingly isolating Canada even more."

    The government said Canada will not attend an international scientific conference on the convention taking place this month in Bonn, Germany. Dewar surmised that "maybe they were concerned because we hadn't been doing enough. Maybe they were concerned because they were going to be asked to do more. I don't know. … It's a real head scratcher." http://scim.ag/Candes

    Graz, Austria

    ESA Eyes Forest-Measuring Space Mission

    CREDIT: © ESA/P. CARRIL, 2012

    Biomass, a mission to measure the carbon content of the world's forests, is likely to get the go-ahead from the European Space Agency (ESA). Last month, the agency selected the €420 million mission over two other candidates, according to Volker Liebig, ESA's head of Earth observation. But the final decision rests with ESA's Earth Observation Programme Board, made up of representatives from ESA's 20 member states, which will meet in early May.

    Biomass will use radio waves to assess the amount of material in a forest. Radio waves at different polarizations bounce off different parts of the forest canopy and soil; by measuring the power and phase of the reflected polarized beams, Biomass can calculate the mass, height, and structure of the forest.

    Land-use change is one of the key sources of atmospheric carbon dioxide. Biomass will be able to measure the loss of carbon from deforestation and the effectiveness of reforestation. "It changes the game completely," says Shaun Quegan, chair of the Biomass mission advisory group. "We'll be able to see things we've never seen before."

    Shanghai, China

    New Avian Flu Kills Two

    China's National Health and Family Planning Commission reported two deaths in Shanghai on 31 March from an avian influenza virus not previously identified in humans. The flu virus, H7N9, killed two men, ages 87 and 27, and infected a woman in nearby Anhui province.

    It is unknown whether the outbreak originated in poultry or wild birds, says George F. Gao, deputy director-general of the China Center for Disease Control and Prevention (China CDC) in Beijing. China CDC researchers have sequences from two different strains of H7N9 and are now investigating the possibility of human-to-human transmission, Gao says. Although there is no evidence that the virus is airborne, he says, the possibility has not yet been ruled out.

    The disparate locations of the three patients "would imply that the virus itself is also widespread in the animal population," says Malik Peiris, a virologist at the University of Hong Kong. To avoid "a situation like H5N1, where the virus becomes entrenched," he adds, any animal outbreaks must be quickly contained. http://scim.ag/avianflu2

  2. Newsmakers

    Three Q's

    CREDIT: COURTESY OF WHOI

    Hollywood director James Cameron donated his submersible Deepsea Challenger, which he rode to the bottom of the Mariana Trench last year, to the Woods Hole Oceanographic Institution (WHOI) in Massachusetts last week. WHOI Director of Special Projects David Gallo talks about plans for the sub.

    Q:What's next for the Deepsea Challenger?

    D.G.:We're still beginning to understand exactly what's on that submarine. The cameras, the lights, the power—all of these things are advances for us.

    Q:Which of Deepsea Challenger's technologies will WHOI focus on in the near term?

    D.G.:Robotics. We've got a robotics system, the Nereus system, that's good to go. Before Jim made this offer, we were already heading to the deepest ocean. This is a real windfall for us, to be able to talk to Jim's team … and find out what components of Jim's dream can be used on our robots. [And] we plan on using his cameras and lighting this June in the Caribbean to explore some of its very deepest spots.

    Q:Why use Deepsea Challenger rather than, for example, Alvin?

    D.G.:[Deepsea] Challenger opens up the entire ocean, even the deepest trenches [about 11,000 meters deep], to exploration. [Alvin can dive to 4500 meters.] There're all these different challenges about working deep, and Jim's done that homework for us.

    We get hung up a lot on the tangible submarine, but this collaboration is as much about what we're going to do together in the future. … We're looking at creating a whole new breed of scientific equipment to explore and open up the deep ocean. http://scim.ag/WHOIChal

    Marcia McNutt to Head Science

    CREDIT: COURTESY OF MARCIA MCNUTT

    Geophysicist Marcia McNutt, who stepped down as head of the U.S. Geological Survey (USGS) in February, has been tapped to be the new editor-in-chief of Science. McNutt will take over the editorship on 1 June from Bruce Alberts, who announced his retirement last year.

    McNutt is no stranger to Science: She served on Science's Senior Editorial Board, which helps set journal policy, from 2000 to 2009, an experience that she says will be helpful in her new job on several fronts. "It gave me a chance to understand at a high level a lot of the decisions that the editor-in-chief is responsible for," including the balance of content between news and research or between different disciplines.

    Before she was appointed as director of USGS in 2009, McNutt was president and CEO of California's Monterey Bay Aquarium Research Institute for 12 years. http://scim.ag/McNuttSci

  3. Random Sample

    Obama Announces $100 Million Brain Project

    CREDIT: MISHA B. AHRENS AND PHILIPP J. KELLER

    President Barack Obama announced on 2 April that his fiscal year 2014 budget request will include a $100 million initiative to map human brain activity, a project that he says could lead to cures for diseases such as epilepsy and autism, although some scientists question the effort's rationale (Science, 1 March, p. 1022). The BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative, he said, will "give scientists the tools they need to get a dynamic picture of the brain in action." Complex brain functions and disorders alike emerge from millions of cells working together, so the initiative aims to develop new technologies that can monitor large groups of neurons firing simultaneously. (Pictured: neurons firing, in red, in a zebrafish larva brain). If approved by Congress, the project will be funded by the National Institutes of Health (NIH) Blueprint for Neuroscience project, the Defense Advanced Research Projects Agency, and the National Science Foundation. An NIH working group co-chaired by Cornelia Bargmann of Rockefeller University and William Newsome of Stanford University will better define the project.

    They Said It

    "It was becoming clear that there were people in NASA who would be much happier if the 'sideshow' would exit."

    —Climate scientist and activist James Hansen in an e-mail to The New York Times, announcing his departure from NASA this week after 46 years at the administration.

    Antarctic Blue Whales Tracked by Their Songs

    CREDIT: © MICK DAVIDSON

    The Remora pulled to within 8 meters of the whale, trying to stay ahead to give marine mammal ecologist Virginia Andrews-Goff a good chance of attaching a satellite tag to the leviathan. "You're … looking/feeling for that correct spot, the correct angle and the correct moment during the whale's surfacing to deploy the tag," she says. "Afterwards I was in awe and feeling incredibly small."

    Andrews-Goff is part of a team of scientists from the Australian Antarctic Division in Kingston that has successfully managed, for the first time, to track the world's largest creatures—the Antarctic blue whale—using only its sound. Researchers have long used the whales' distinctive voices to study the animals, but developing a passive acoustic tracking system that could find them in real time was a trickier problem. Led by Brian Miller, the team last year tested hydrophone-bearing sonobuoys, very high frequency radio receivers, and custom software that successfully pinpointed pygmy blue whales by their songs at distances of more than 60 kilometers.

    But the big success came this year, during the 47-day inaugural Southern Ocean trip of the Antarctic Blue Whales Project. Researchers were able to detect the "very deep and resonating song" of the blue whale from 600 nautical miles away, Andrews-Goff says. They recorded 626 hours of sound, analyzing 26,545 calls. The team also used those calls to triangulate the positions of the whales, so that they could collect photo IDs as well as biopsy samples. They were also able to place satellite tags on two whales. The overall goal of the program, part of the international Southern Ocean Research Partnership, is to estimate the blue whales' abundance and distribution, Andrews-Goff says. The information will be shared with the International Whaling Commission to aid conservation efforts.

    ScienceLIVE

    Join us on Thursday, 11 April, at 3 p.m. EDT for a live chat on genetic privacy. How safe is your genome? http://scim.ag/science-live

  4. The Deep Earth Machine Is Coming Together

    1. Richard A. Kerr

    Researchers studying how Earth's deep interior works are recognizing a new part connecting the depths to the surface, though the depths remain mysterious.

    Earth is an engine fueled by its own heat. Now, after sharpening their view of the planet's rocky inner workings for almost a century, scientists are finally glimpsing how the Earth engine as a whole is working.

    Since the plate tectonics revolution, researchers have recognized surface geology for what it is: a cold, rocky scum of continent-carrying, ocean-crust-covered tectonic plates. And the coldest, densest pieces of those ocean plates were clearly plunging into the barely yielding rocky interior, or mantle, toward the even hotter, molten core.

    But the nature of whatever might be carrying heat and material back toward the surface has been hotly debated for 40 years. Could towering plumes of hotter-than-normal rock be rising like lava lamp blobs from near the core? That could explain a range of geologic oddities, including the construction of monstrous piles of lava like Hawaii and mass extinctions seemingly linked to massive volcanic eruptions. Decades of study—imaging the mantle with seismic waves, divining the nature of the depths through geochemistry, and modeling the workings of the mantle the way meteorologists forecast the weather—now appear to be paying off.

    Birds of a feather.

    Rising plumes likely connect huge volcanic eruptions (LIPs), diamond-pipe eruptions (kimberlites), and hot spots to two piles (pink, LLSVPs) on the bottom of the mantle.

    CREDIT: T. H. TORSVIK ET AL., NATURE 466, 7304 (2010)

    "I'm finally off the fence," says seismologist Eugene Humphreys of the University of Oregon in Eugene. Humphreys thinks he can "see," through seismic eyes, a plume that's been delivering the heat that drives eruptions around Wyoming's Yellowstone National Park. It is the first such feature—fed from the deepest reaches of the mantle—that looks like it will receive wide acceptance.

    Along with recent work connecting plate tectonics to the deep interior, the recognition of such plumes is finally forging a strong link that spans the mantle from bottom to top. Plumes of all sizes seem to rise from two huge piles of who-knows-what sitting 2900 kilometers down at the bottom of Earth's mantle embedded in a mystery layer hundreds of kilometers thick. The outline of an operating manual is coming into view, but some pieces of the Earth engine are yet to be labeled.

    Through a glass, darkly

    Earth's interior didn't always seem so messy, or so interesting. By the middle of the last century, seismologists had divided the planet's 2900-kilometer-thick mantle into a half dozen layers on the basis of how seismic waves passed through the rock. Each layer, as far as could be told, kept to itself. But then in the 1960s, plate tectonics came along. Central to the revelation of drifting continents was the realization that the planet's uppermost layer—the hundred kilometers or so of cold, rigid, crust-topped mantle constituting plates—was diving into deep-sea trenches and thus into the next layer down, the upper mantle.

    Seismologists' next impenetrable boundary took longer to puncture. With more and better seismic records, researchers could trace descending plates, called slabs, much deeper using a technique called tomography. Because seismic waves speed up in cold rock, scientists can use them to form tomographic images of the descending slabs, much as they use x-rays in CT scans of the body. By the 1990s, seismologists could see some slabs struggling to pierce the supposed barrier between the upper mantle and the lower mantle 660 kilometers down—and then, once through, heading for the bottom (Science, 31 January 1997, p. 613).

    But what about plumes? Deep thinkers of the 1970s had invoked them as a way of explaining the Hawaiian volcanoes and a host of other volcanic hot spots from Iceland to Soma. Were seismologists of the 2000s catching plumes in their tomographic images of the mantle? "I would say no," Humphreys says. A few seismologists would disagree, arguing that by dint of extra observations or special tomographic techniques they could image plumes stretching from the core-mantle boundary up to dozens of hot spots (Science, 22 September 2006, p. 1726).

    Seismologist Jeroen Ritsema of the University of Michigan, Ann Arbor, sides with the doubters. That's because he and colleagues have quantitatively considered just how hard it is to image plumes. "I hate to say this about my own work," he says, "but tomography is not simple. You get very easily fooled." Yong Keun Hwang of Michigan, Ritsema, and colleagues reported in Geophysical Journal International in August 2011 how a long list of factors works against seeing plumes: their expected narrowness; their relative warmth, which disperses seismic waves; the confounding effect of wave-bending variations in rock of the uppermost mantle; and on and on.

    Things looking up anyway

    Plumes have long eluded seismologists, but after 40 years, solid-Earth scientists are coming to agree that they exist. "My take is not driven by observations but by fundamental theory," says planetary physicist David Stevenson of the California Institute of Technology (Caltech) in Pasadena. "There's heat coming from the bottom [of the mantle]; the natural way to take care of that is to have material peel away as plumes. I do believe this theoretical argument is quite a strong one."

    Mantle geochemists have their own line of argument supporting plumes. They have measured the trace elements, noble gases, and isotopes of rock brought to the surface in eruptions at hot spot volcanoes that have become ocean islands. They find that what goes down into the mantle—the ocean crust on slabs and sediments, mostly—can come back up eons later in the magma that builds ocean islands. And then there are the hot spot ocean islands that pop up one after the other in a line as an ocean plate passes over, like a smokestack blowing smoke into the passing breeze. "None of that is easy to do unless you accept plumes," says geochemist Stanley Hart, a scientist emeritus from Woods Hole Oceanographic Institution in Massachusetts. "I'm getting pretty close" to seeing plumes as unavoidable, he says.

    In the past decade, even some geoscientists concerned mostly with the jostling of plate tectonics on the surface have embraced deep plumes. In a 2010 Nature paper, paleomagnetician Trond Torsvik and tectonophysicists Bernhard Steinberger of the University of Oslo and Kevin Burke of the University of Houston and colleagues summarized 10 years of work connecting some of Earth's surface scum to those two piles of geocrud at the bottom of the mantle, one pile lying beneath Africa and the other under the South Pacific. Paleomagneticians measure the faint magnetic field locked into rocks when they form at the surface. They can then infer where a rock formed before plate motions carried it away to its present location.

    In effect, Torsvik and his colleagues ran the plate tectonics part of the Earth machine backward (mathematically) for more than 200 million years. They wanted to see where, in relation to the interior, geologic features possibly related to plumes originally formed. Geochemistry and chain formation hint that 11 currently active hot spots may be deeply rooted in the mantle. Torsvik and his colleagues found that 10 of the 11 formed over or around the edge of a pile. Twenty-three of 25 so-called Large Igneous Provinces (LIPs)—huge piles of a few million cubic kilometers of lava like the Siberian Traps—erupted over the edges of piles. And 80% of kimberlite "pipes" through which diamond-bearing minerals were blasted to the surface from 100 kilometers down also erupted over a pile.

    "That's a very strong geographical association," says geochemist Albrecht Hofmann, who is a geochemist emeritus at the Max Planck Institute for Chemistry in Mainz, Germany. "The association with the edges of two huge blobs strongly says there's a causal connection." The geodynamicists who run computer models simulating Earth's inner churnings approve of that idea. "We can get plumes off the edges" of the piles, says geodynamicist Michael Gurnis of Caltech. "That seems reasonable."

    All churned up.

    In this computer simulation, cold slabs (yellow cored with light blue) of tectonic plate (dark blue when covering globe) descend into the mantle while hot plumes (red) rise from near the hot core.

    CREDIT: FABIO CRAMERI AND PAUL J. TACKLEY, ETH ZURICH

    These three lines of evidence—geodynamical, geochemical, and geological—have moved the community toward the reality of plumes, seismological smoking gun or no. "There's a comfort level with there being some material [at the surface] from the very deep Earth," says Thorne Lay, a seismologist at the University of California (UC), Santa Cruz. And deep plumes are the only way anyone can imagine that happening.

    There have been dissenters, of course. A small cadre of researchers has advocated, often energetically, nonplume explanations for supposed plume phenomena (see www.mantleplumes.org). But "the plume deniers are fading," says retired geochemist Hart. "The major forces are getting older, and none of the young guys are picking it up." Plume critics aren't writing peer-reviewed papers, he says, so "I don't argue with them anymore; it's a distraction."

    Mantle shepherding.

    In this computer simulation, cold descending slabs (blues) have herded dense mantle-bottom detritus into a pile or LLSVP (brown) from which hot plumes are rising.

    CREDIT: D. BOWER & M. GURNIS, CALIFORNIA INSTITUTE OF TECHNOLOGY

    One relatively new and still emerging piece of evidence supporting plumes—published on 15 May 2012 in Earth and Planetary Science Letters—comes from seismologists, as a group the most cautious about accepting them. Brandon Schmandt of the University of New Mexico and his colleagues, including Humphreys, drew on observations from a unique source, the Transportable Array (Science, 25 September 2009, p. 1620)—an 800-kilometer-wide array of 400 seismometers stretched between the Canadian and Mexican borders—supplemented by other seismometers near Yellowstone. The combined observations provided the sharpest and deepest view by far of what lies beneath the Yellowstone hot spot.

    In no uncertain terms, Schmandt and colleagues' paper announced a hot mantle upwelling beneath Yellowstone. Their tomographic imaging used two different kinds of seismic waves to show extra-hot mantle rock extending down through the 660-kilometer-deep boundary between the upper and lower mantle to a depth of 900 kilometers, below which even their dense data set would not show a plume even if it were there. And using another seismic technique to gauge the depth to the upper-lower mantle boundary, the group found the boundary—a temperature-sensitive change of mineral crystal structure or phase change—to be raised by 12 to 18 kilometers from its normal level across the same area that tomography shows to be extra hot.

    Taken together, the results require a hot plume rising beneath Yellowstone, Humphreys says. And thermodynamics requires an origin near the core. "It's all coming from a source associated with cooling of the core," he says, adding, "it's kind of sad that what it took was more measurements and not more cleverness, but that's the case."

    Seismologist Barbara Romanowicz of UC Berkeley is impressed. She had never been convinced that any plume, including the iconic Hawaiian plume (Science, 4 December 2009, p. 1330), had been shown to rise from the deep mantle. In a 19 February interview with Science, she said she was, as Humphreys had been, still "sitting on the fence." But after hearing Schmandt present the Yellowstone work at a seminar later that week, she came down off the fence. She found the two types of seismic data "quite convincing" that at least one deep plume rises into the upper mantle.

    About that crud on the bottom

    If slabs are falling through the full depth of the mantle and plumes are rising from the bottom, then what, exactly, is going on down there at the deep end of the Earth engine? Seismologists have identified several different-looking sorts of geocrud sitting on the bottom. There are the two piles (technically called Large Low-Shear Velocity Provinces or LLSVPs, but who can pronounce that?). Seismology sizes up the piles as thousands of kilometers across and perhaps a few hundred kilometers high, made of somewhat different stuff from their surroundings.

    Far smaller Ultra-Low Velocity Zones (ULVZs) tend to crowd around the piles but rise only 10 or 20 kilometers above the core-mantle boundary. And then there's the core-enveloping D″ (pronounced "D double prime") layer topping out a few hundred kilometers above the core.

    Just what these seismic features might be hasn't gotten much clearer since their discovery up to half a century ago. Mineral physicists squeezing and heating rock in the laboratory have lately found that iron-rich minerals—presumably enriched by iron from the core—might explain ULVZs, although some still favor partial melting of the rock. The mineral physicists also found a phase change that may explain the seismic upper boundary of D″, but what lies below it remains mysterious. And the composition of the piles is still anyone's guess.

    Stuck for the moment, researchers can turn to geodynamics. In the past few years, mantle modelers—including Paul Tackley of ETH Zurich in Switzerland; Shijie Zhong of the University of Colorado, Boulder; Allen McNamara of Arizona State University, Tempe; and Caltech's Gurnis—have run simulations to see what would be the fate of anything dense enough to settle to the bottom of the mantle. In models of the mantle, slabs that are now descending in a ragged curtain from pole to pole provide the dominant driving force. Slabs churn the mantle from top to bottom, shearing any hapless slabs, sediments, or other tectonic detritus caught in midmantle into a 2900-kilometer-thick marble cake of rock.

    In the models, the curtain of descending slabs tends to herd those slabs dense enough to reach the bottom intact and anything else already there into two antipodal structures near the equator. These structures bear a strong resemblance in shape and location to the current piles.

    But what besides old slabs (it takes 100 million years or so to make the trip) might be down there? The leading candidate comes from the geochemists, who see it as a storage locker for rock left from the first 1% of the planet's history. They find the barest of hints of such primitive stuff in the isotopes of noble gases from ocean islands and in the isotopes of the lanthanide element neodymium from ancient continental rocks (Science, 6 October 2006, p. 36).

    Prospects for consensus on the bottommost mantle are guarded. Seismologists will be markedly sharpening their tomographic imaging in the next 5 years, Romanowicz says, but sniffing out composition will remain a challenge. Mineral physicists are already pushing the envelope in the lab, although calculations of mineral properties from first principles may one day surpass lab work. And geochemists would like to find some more elements carrying clues to the nature of the deep mantle.

  5. Molecular Biology

    'Dead' Enzymes Show Signs of Life

    1. Mitch Leslie

    Pseudoenzymes can't catalyze chemical reactions, but researchers are discovering that they perform a variety of other cellular jobs.

    Biologists were taken aback about a decade ago when they began to realize that a large fraction of human enzymes appear to be duds. That realization was a shock because we can't live without the enzymes that promote biochemical reactions. So how could so many of these critical molecules have lost their key function? And why does the body keep on producing apparently inert proteins?

    One of the first indications that such "pseudoenzymes" are abundant came in 2002, when a research team combed through the newly available human genome sequence to identify all genes that encode protein kinases. These influential enzymes serve as switches in molecular circuits inside cells, transferring phosphate groups onto a variety of targets to help control a wide range of activities, such as metabolism and cell movement.

    Of the 518 human protein kinases encoded by our DNA, about 10% lacked at least one of three key amino acids necessary for catalyzing the phosphate transfer and thus seemed to be inert, the scientists reported (Science, 6 December 2002, p. 1912). Although defunct enzymes had come to light before, the large number of these pseudokinases, as scientists dubbed them, was a shock, says team leader Gerard Manning, now director of bioinformatics and computational biology at Genentech in South San Francisco, California. "We thought we must have got it wrong."

    They had it right, further studies have revealed. Almost every enzyme family includes seemingly inactive members, and in some clans, such as the sulfotransferases that swap sulfate groups, more than half the proteins encoded by our genome show signs of being catalytically compromised. And "dead" enzymes show up in organisms as diverse as bacteria, plants, and the mites that cause the skin condition scabies.

    The pseudoenzyme genes that Manning and others identified are not degraded DNA. Cells make these proteins, and the DNA sequences for them have changed little over millions of years of evolution. That constancy suggests that the proteins have functions. "Biological systems don't bother keeping these proteins unless they are doing something important," says biochemist Patrick Eyers of the University of Sheffield in the United Kingdom.

    Sure enough, many supposedly inactive enzymes are gainfully employed in organisms—not as catalysts, but in a variety of other roles, researchers are now finding. Some help "true" enzymes catalyze biochemical reactions by forcing them into the correct shape. Others provide platforms where proteins can mingle. Still others join with receptors to help cells communicate, serve as bodyguards that escort proteins to new locations, or perform other tasks. "They turn out to be biologically really important," says protein chemist Susan Taylor of the University of California, San Diego. "They have been conserved for a reason."

    CREDIT: HAL MAYFORTH

    Biochemist Daan van Aalten of the University of Dundee in the United Kingdom terms the DNA sequences encoding pseudoenzymes "the forgotten genes" because most researchers have overlooked them. But molecular biologists are now looking to the proteins encoded by these genes for insights into enzyme evolution. Drug designers hope to exploit them to create safer, more specific medications. And pseudoenzymes are causing biochemists to rethink some of their ideas about how conventional enzymes work. "If I were starting out again, I'd work on these [pseudoenzymes]," says biochemist Dario Alessi, also of the University of Dundee.

    A pseudoenzyme is born

    To study pseudoenzymes, researchers first have to recognize them, but that isn't always straightforward. A candidate's amino acid sequence can indicate, but not confirm, that it's catalytically compromised. So researchers often determine the protein's 3D structure, test whether it can perform the expected biochemical reaction for an enzyme of its class, and conduct other experiments. Even then, the evidence is not always decisive (see sidebar, p. 27).

    Despite the uncertainties, the consensus is that many proteins that look like enzymes primarily perform functions that don't involve catalyzing reactions. The majority of these pseudoenzymes are closely related to active enzymes, and researchers have proposed two evolutionary explanations for such connections. Both involve a gene duplication at some time in the past.

    In what researchers think is the more common scenario, the original and duplicated genes coded for an enzyme, and mutations corrupted the active site of one of the copies to produce a pseudoenzyme. "It's extremely easy to lose enzyme function because the catalytic residues [amino acids] are so well conserved," says computational biologist Janet Thornton, director of the European Bioinformatics Institute in Hinxton, U.K.

    In some cases, the process may also operate in the opposite direction, Alessi says. "My theory is that an active kinase might have evolved from a pseudokinase." In this scenario, the pseudoenzyme was already around, handling some noncatalytic cellular job, when its gene duplicated. Mutations then conferred catalytic ability on one of the versions, creating a working enzyme. A few dead enzymes do seem to have been the ancestors of living ones: Their functional descendants are recognizable because other members of the immediate family are not enzymes.

    Finding good help

    Cells teem with perfectly good proteins, so why did they enlist defective enzymes to perform vital duties? Those pseudoenzymes that evolved from functional enzymes might have lost their catalytic ability, but they retained other talents. Before an enzyme instigates a chemical reaction, for instance, it grabs its target molecule, or substrate. Their inactive descendants often keep this binding ability, meaning they can home in on the protein for other purposes. Dead enzymes share other similarities with their active kin, notes cell biologist Matthew Freeman of the University of Oxford in the United Kingdom. They often hang out in the same tissues as their active counterparts and at the same time. Thus, a pseudoenzyme "is perfectly poised to have a regulatory role" and help control biochemical reactions, says biochemist Margaret Phillips of the University of Texas Southwestern Medical Center in Dallas. In many cases, Freeman says, researchers have established that pseudoenzymes regulate the reactions that involve their active relatives.

    Pseudoenzymes on the brain.

    Toxoplasma parasites, shown here in a brain cyst, rely on pseudoenzymes to escape immune attacks.

    CREDIT: CDC

    STRADα shows how a pseudoenzyme's binding ability enables it to regulate other enzymes. It latches onto and adjusts the activity of LKB1, a tumor suppressing kinase that's inactive in certain cancers. In a 2009 Science paper, Alessi, van Aalten, and colleagues showed how STRADα works. With help from a third protein, MO25α, STRADα locks LKB1 into its active pose, allowing it to perform its job (Science, 18 December 2009, p. 1707). The work suggests that "it's possible for a pseudokinase to activate a downstream kinase by binding it," van Aalten says.

    The iRhom pseudoenzymes that Freeman and colleagues study are also regulators, and they operate in two physiological contexts—antipathogen defense and sleep—that are so dissimilar "it's almost embarrassing," he says. Their defensive role involves the secretion of TNFα, an inflammation-promoting molecule that various body cells emit when microbes menace. The release mechanism is involved. A cell first dangles a molecule of TNFα from its plasma membrane, and then an enzyme known as TACE snips the TNFα free. But to get into position to make the cut, TACE has to travel from the cellular organelle called the endoplasmic reticulum to the plasma membrane. Last year, Freeman's group and another led by immunologist Tak Mak of the University of Toronto in Canada revealed that iRhom2 binds to TACE in the endoplasmic reticulum and enables the enzyme to leave the organelle (Science, 13 January 2012, pp. 225 and 229). Without iRhom2, TACE doesn't depart, leading to reduced TNFα secretion and weakened immune defenses. Mice lacking iRhom2 are more susceptible to bacterial infections.

    Going over to the enemy

    Pathogens also take advantage of pseudoenzymes. Phillips and colleagues have discovered, for example, that dead enzymes are crucial for Trypanosoma brucei, the parasite that causes African sleeping sickness in people. Pseudoenzymes increase the activity of two of the parasite's key metabolic enzymes by up to 3000 times.

    One of the world's most widespread parasites, Toxoplasma gondii, also deploys pseudoenzymes, using them to help confound immune defenses of one of its hosts. Toxoplasma dwells in nearly one-third of the world's human population, usually without causing distress, but people aren't the only stopovers during the parasite's life cycle. "Toxoplasma is highly unusual in being able to infect virtually any bird or mammal," says molecular biologist John Boothroyd of the Stanford University School of Medicine in California. Rodents, which are one of the parasite's hosts, fight back against Toxoplasma with proteins from the IRG family. They coat the capsules in which the parasites lurk, killing the organisms inside. To protect itself, the parasite releases a catalytically active enzyme, ROP18, that disrupts IRG proteins.

    Last year, Boothroyd's group and two others reported that a Toxoplasma pseudoenzyme called ROP5 partners with ROP18 in the fight against IRG proteins. ROP5 latches onto an IRG protein and clamps it in a shape that is vulnerable to attack by ROP18. Boothroyd says that he likens ROP5 to "the bully's side-kick who holds the kid in the schoolyard while the bully beats him up."

    ROP5 helps ROP18 hit back in other ways, too. The group led by microbiologist L. David Sibley of Washington University School of Medicine in St. Louis found that ROP5 also holds ROP18 in its active shape so that it can neutralize the defensive proteins. It's not surprising that Toxoplasma turned to a pseudoenzyme to assist ROP18, says Boothroyd's co-author Michael Reese, a biochemist also at the Stanford University School of Medicine. The parasite is rife with dead enzymes—among the organisms whose genomes researchers have sequenced, Toxoplasma has the highest proportion of pseudokinases, Reese notes.

    The parasites can carry more than 10 copies of the ROP5 gene that differ only slightly from one another, possibly revealing an evolutionary battle with their host's immune system, Sibley says. You'd expect that mice would evolve slightly different IRG proteins that are better weapons against Toxoplasma and that the parasites would respond by tweaking the ROP proteins and creating new versions. But mutations that modify ROP18's amino acid sequence could undermine its function, so allowing ROP5 to change might be a safer strategy, Sibley says. Without a catalytic site than can be compromised, he notes, "it doesn't matter if it's peppered with a lot of mutations."

    Getting practical

    Given their ability to regulate active enzymes, pseudoenzymes have promise as drug targets, some scientists suggest, although no such drugs are in use. Going after dead kinases, Eyers says, may offer alternatives to traditional kinase inhibitors, a fast-growing drug class responsible for nearly $11 billion in sales in the United States alone. Probably the most famous kinase inhibitor is Gleevec, which reached the clinic in 2001 and has proven successful against chronic myelogenous leukemia.

    The drawback of such inhibitors is that because the kinase active site is so similar across enzymes, drugs that block one kinase can interfere with others, triggering side effects. Gleevec, for example, can cause abdominal pain, nausea, fatigue, and other problems. But indirectly blocking an overactive kinase that has pathogenic effects by targeting its pseudoenzyme partner might leave other kinases unscathed. However, some remain skeptical that pseudoenzymes are worth aiming at, notes biochemist Mark Lemmon of the University of Pennsylvania. Researchers have a lot of experience designing drugs to block kinases, but devising one that disables a pseudokinase is a challenge because the traditional and well-studied enzyme active site isn't the natural place to hit. "They could still be very important drug targets," he says. "We just have to think differently" about how to inhibit them.

    Even if pseudoenzymes haven't yet made much of a practical impact, they've had an intellectual effect, according to Eyers. "Pseudokinases have made us think, 'We really don't know so much about kinases,'" he says. As a result, biochemists are taking a second look at basic questions, such as how much activity an enzyme has to show to be considered functional. At a broader level, the discovery of this new category of inactive enzymes reveals how little researchers understand about parts of the genome, Freeman says. "I'm intrigued by the concept that there are a lot of genes that we know nothing about."

  6. Dead or Alive?

    1. Mitch Leslie

    The enzymatic competence of proteins can be difficult to judge, and some apparent pseudoenzymes have fooled researchers.

    The enzymatic competence of proteins can be difficult to judge, and some apparent pseudoenzymes have fooled researchers. Take CASK, a protein found in neurons that is one of the original “nonfunctional” kinases pinpointed by Gerard Manning, director of bioinformatics and computational biology at Genentech in South San Francisco, California, and colleagues (see main story, p. 25). Kinases typically swipe a phosphate group from the molecule adenosine triphosphate (ATP) and pass it to another protein. CASK lacks two key amino acids that researchers thought were necessary for transferring a phosphate, which suggested that it's a prototypical pseudokinase.

    CREDIT: K. MUKHERJEE ET AL., CELL 133, 2 (2008)

    But after determining the crystal structure of a portion of the protein (right), neuroscientist Konark Mukherjee, now at the Virginia Polytechnic Institute and State University Carilion Research Institute in Roanoke, and colleagues reported that CASK can use alternative amino acids to instigate the kinase reaction. In Cell in 2008, the team also revealed evidence from test tube experiments and cultured cells that suggests that CASK serves as a catalyst, albeit a weak one. Whether that's the biological role of CASK remains unclear, however, leaving its pseudostatus up in the air.

    Researchers sometimes get similarly fooled into thinking a protein is an enzyme. Early biochemical studies suggested enzyme activity for integrin-linked kinase (ILK), a potential drug target because mutated versions promote cancer. Drug developers even began trying to identify inhibitors under the assumption that it was a functioning kinase, says structural biologist Jun Qin of the Cleveland Clinic Foundation in Ohio.

    Yet when he and his colleagues figured out the 3D structure of a fragment of ILK attached to its activator, they found that ILK's ATP-binding site was far from the part of the protein that would catalyze a reaction, making the phosphate handover unlikely. “We now know it has no kinase function,” says Qin, whose team reported its findings in Molecular Cell in 2009. Instead, buttressing its pseudoenzyme designation, ILK links to other proteins to form a relay between a cell's skeleton and receptors on its surface.

Log in to view full text