네이처 컨텐츠

Editorials

Look after the pennies p.269

Government decisions about where to spend and where to cut should be based on evidence, not ideology.

doi: 10.1038/496269a

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Smoke and mirrors p.269

Italy’s parliament must listen to expert advice before deregulating stem-cell therapies.

doi: 10.1038/496269b

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Due credit p.270

Nature’s podcast charts 12 landmark discoveries in the history of science.

doi: 10.1038/496270a

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News

A back seat for basic science p.277

Translational research wins in Obama’s budget, but its economic value remains uncertain.

Eric Hand, Beth Mole, Lauren Morello, Jeff Tollefson & Meredith Wadman

doi: 10.1038/496277a

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News Features

Splinters of the Amazon p.286

Decades after Thomas Lovejoy isolated fragments of the Brazilian rainforest in a grand experiment, researchers are building on his legacy around the world.

Jeff Tollefson

doi: 10.1038/496286a

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Polio’s moving target p.290

Finding and vaccinating Nigerian nomads may be one of the last obstacles to the eradication of polio.

Ewen Callaway

doi: 10.1038/496290a

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News & Views

A potted history of Japan p.302

The discovery of lipids on ceramic fragments from the Japanese Jōmon period provides the earliest evidence for the use of pottery for cooking and may prompt a rethink of some aspects of human innovation. See Letter p.351

Simon Kaner

doi: 10.1038/nature12093

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A cosmic growth spurt in an infant galaxy p.303

One of the most extreme starburst galaxies in the early Universe has been identified and characterized. This system shows the rapid formation of a massive galaxy when the Universe was only 6% of its current age. See Letter p.329

Desika Narayanan & Chris Carilli

doi: 10.1038/496303a

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A whiff of genome p.304

The relatedness of animals influences their behaviour, but how do they detect their kin? It seems that nasal sensory neurons differentiate between minute structural differences in urinary peptides that reflect genetic variation.

Thomas Boehm

doi: 10.1038/496304a

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Molecular motion watched p.306

A laser pulse can switch certain crystals from an insulating phase to a highly conducting phase. The ultrafast molecular motions that drive the transition have been directly observed using electron diffraction. See Letter p.343

Bradley Siwick & Eric Collet

doi: 10.1038/496306a

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Nitrogen deposition and forest carbon p.307

Human activity, such as agricultural fertilizer use, has increased the amount of nitrogen deposited onto forests from the atmosphere. The photosynthetic response to this in evergreen needleleaf forests has been quantified globally.

Beverly Law

doi: 10.1038/496307a

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Spatial signatures of resilience p.308

Predicting when the dynamics of a complex system will undergo a sudden transition is difficult. New experiments show that the spatial distribution of organisms can indicate when such tipping points are near. See Letter p.355

Stephen R. Carpenter

doi: 10.1038/nature12092

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Articles

The African coelacanth genome provides insights into tetrapod evolution OPEN p.311

Genome sequencing and phylogenomic analysis show that the lungfish, not the coelacanth, is the closest living relative of tetrapods, that coelacanth protein-coding genes are more slowly evolving than those of tetrapods and lungfish, and that the genes and regulatory elements that underwent changes during the vertebrate transition to land reflect adaptation to a new environment.

doi: 10.1038/nature12027

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Gating of the TrkH ion channel by its associated RCK protein TrkA p.317

Here it is shown that ion flux through the TrkH–TrkA complex is upregulated by ATP and downregulated by ADP; solving the X-ray crystal structures of the tetrameric TrkA ring in the absence and presence of TrkH suggests a mechanism by which ATP-induced conformational changes in TrkA augment the activity of TrkH.

Yu Cao, Yaping Pan, Hua Huang, Xiangshu Jin, Elena J. Levin, Brian Kloss & Ming Zhou

doi: 10.1038/nature12056

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The structure of the KtrAB potassium transporter p.323

This study reports the X-ray crystal structure of a Ktr K+ transporter; the structure of this KtrAB complex reveals how the dimeric membrane protein KtrB interacts with the cytosolic octameric KtrA regulatory protein.

Ricardo S. Vieira-Pires, Andras Szollosi & João H. Morais-Cabral

doi: 10.1038/nature12055

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Letters

A dust-obscured massive maximum-starburst galaxy at a redshift of 6.34 p.329

Massive present-day early-type (elliptical and lenticular) galaxies probably gained the bulk of their stellar mass and heavy elements through intense, dust-enshrouded starbursts—that is, increased rates of star formation—in the most massive dark-matter haloes at early epochs. However, it remains unknown how soon after the Big Bang massive starburst progenitors exist. The measured redshift (z) distribution of dusty, massive starbursts has long been suspected to be biased low in z owing to selection effects, as confirmed by recent findings of systems with redshifts as high as ∼5 (refs 2–4). Here we report the identification of a massive starburst galaxy at z = 6.34 through a submillimetre colour-selection technique. We unambiguously determined the redshift from a suite of molecular and atomic fine-structure cooling lines. These measurements reveal a hundred billion solar masses of highly excited, chemically evolved interstellar medium in this galaxy, which constitutes at least 40 per cent of the baryonic mass. A ‘maximum starburst’ converts the gas into stars at a rate more than 2,000 times that of the Milky Way, a rate among the highest observed at any epoch. Despite the overall downturn in cosmic star formation towards the highest redshifts, it seems that environments mature enough to form the most massive, intense starbursts existed at least as early as 880 million years after the Big Bang.

Dominik A. Riechers, C. M. Bradford, D. L. Clements, C. D. Dowell, I. Pérez-Fournon, R. J. Ivison, C. Bridge, A. Conley, Hai Fu, J. D. Vieira + et al.

doi: 10.1038/nature12050

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Unexpected strain-stiffening in crystalline solids p.339

Strain-stiffening—an increase in material stiffness at large strains—is a vital mechanism by which many soft biological materials thwart excessive deformation to protect tissue integrity. Understanding the fundamental science of strain-stiffening and incorporating this concept into the design of metals and ceramics for advanced applications is an attractive prospect. Using cementite (Fe3C) and aluminium borocarbide (Al3BC3) as prototypes, here we show via quantum-mechanical calculations that strain-stiffening also occurs, surprisingly, in simple inorganic crystalline solids and confers exceptionally high strengths to these two solids, which have anomalously low resistance to deformation near equilibrium. For Fe3C and Al3BC3, their ideal shear strength to shear modulus ratios attain remarkably high values of 1.14 and 1.34 along the (010)[001] and slip systems, respectively. These values are more than seven times larger than the original Frenkel value of 1/2π (refs 4, 5) and are the highest yet reported for crystalline solids. The extraordinary stiffening of Fe3C arises from the strain-induced reversible ‘cross-linking’ between weakly coupled edge- and corner-sharing Fe6C slabs. This new bond formation creates a strong, three-dimensional covalent bond network that resists large shear deformation. Unlike Fe3C, no new bond forms in Al3BC3 but stiffening still occurs because strong repulsion between Al and B in a compressed Al–B bond unsettles the existing covalent bond network. These discoveries challenge the conventional wisdom that large shear modulus is a reliable predictor of hardness and strength of materials, and provide new lessons for materials selection and design.

Chao Jiang & Srivilliputhur G. Srinivasan

doi: 10.1038/nature12008

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Mapping molecular motions leading to charge delocalization with ultrabright electrons p.343

Ultrafast processes can now be studied with the combined atomic spatial resolution of diffraction methods and the temporal resolution of femtosecond optical spectroscopy by using femtosecond pulses of electrons or hard X-rays as structural probes. However, it is challenging to apply these methods to organic materials, which have weak scattering centres, thermal lability, and poor heat conduction. These characteristics mean that the source needs to be extremely bright to enable us to obtain high-quality diffraction data before cumulative heating effects from the laser excitation either degrade the sample or mask the structural dynamics. Here we show that a recently developed, ultrabright femtosecond electron source makes it possible to monitor the molecular motions in the organic salt (EDO-TTF)2PF6 as it undergoes its photo-induced insulator-to-metal phase transition. After the ultrafast laser excitation, we record time-delayed diffraction patterns that allow us to identify hundreds of Bragg reflections with which to map the structural evolution of the system. The data and supporting model calculations indicate the formation of a transient intermediate structure in the early stage of charge delocalization (less than five picoseconds), and reveal that the molecular motions driving its formation are distinct from those that, assisted by thermal relaxation, convert the system into a metallic state on the hundred-picosecond timescale. These findings establish the potential of ultrabright femtosecond electron sources for probing the primary processes governing structural dynamics with atomic resolution in labile systems relevant to chemistry and biology.

Meng Gao, Cheng Lu, Hubert Jean-Ruel, Lai Chung Liu, Alexander Marx, Ken Onda, Shin-ya Koshihara, Yoshiaki Nakano, Xiangfeng Shao, Takaaki Hiramatsu + et al.

doi: 10.1038/nature12044

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Terrestrial water fluxes dominated by transpiration p.347

Renewable fresh water over continents has input from precipitation and losses to the atmosphere through evaporation and transpiration. Global-scale estimates of transpiration from climate models are poorly constrained owing to large uncertainties in stomatal conductance and the lack of catchment-scale measurements required for model calibration, resulting in a range of predictions spanning 20 to 65 per cent of total terrestrial evapotranspiration (14,000 to 41,000 km3 per year) (refs 1, 2, 3, 4, 5). Here we use the distinct isotope effects of transpiration and evaporation to show that transpiration is by far the largest water flux from Earth’s continents, representing 80 to 90 per cent of terrestrial evapotranspiration. On the basis of our analysis of a global data set of large lakes and rivers, we conclude that transpiration recycles 62,000 ± 8,000 km3 of water per year to the atmosphere, using half of all solar energy absorbed by land surfaces in the process. We also calculate CO2 uptake by terrestrial vegetation by connecting transpiration losses to carbon assimilation using water-use efficiency ratios of plants, and show the global gross primary productivity to be 129 ± 32 gigatonnes of carbon per year, which agrees, within the uncertainty, with previous estimates. The dominance of transpiration water fluxes in continental evapotranspiration suggests that, from the point of view of water resource forecasting, climate model development should prioritize improvements in simulations of biological fluxes rather than physical (evaporation) fluxes.

Scott Jasechko, Zachary D. Sharp, John J. Gibson, S. Jean Birks, Yi Yi & Peter J. Fawcett

doi: 10.1038/nature11983

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Earliest evidence for the use of pottery p.351

Pottery was a hunter-gatherer innovation that first emerged in East Asia between 20,000 and 12,000 calibrated years before present (cal bp), towards the end of the Late Pleistocene epoch, a period of time when humans were adjusting to changing climates and new environments. Ceramic container technologies were one of a range of late glacial adaptations that were pivotal to structuring subsequent cultural trajectories in different regions of the world, but the reasons for their emergence and widespread uptake are poorly understood. The first ceramic containers must have provided prehistoric hunter-gatherers with attractive new strategies for processing and consuming foodstuffs, but virtually nothing is known of how early pots were used. Here we report the chemical analysis of food residues associated with Late Pleistocene pottery, focusing on one of the best-studied prehistoric ceramic sequences in the world, the Japanese Jōmon. We demonstrate that lipids can be recovered reliably from charred surface deposits adhering to pottery dating from about 15,000 to 11,800 cal bp (the Incipient Jōmon period), the oldest pottery so far investigated, and that in most cases these organic compounds are unequivocally derived from processing freshwater and marine organisms. Stable isotope data support the lipid evidence and suggest that most of the 101 charred deposits analysed, from across the major islands of Japan, were derived from high-trophic-level aquatic food. Productive aquatic ecotones were heavily exploited by late glacial foragers, perhaps providing an initial impetus for investment in ceramic container technology, and paving the way for further intensification of pottery use by hunter-gatherers in the early Holocene epoch. Now that we have shown that it is possible to analyse organic residues from some of the world’s earliest ceramic vessels, the subsequent development of this critical technology can be clarified through further widespread testing of hunter-gatherer pottery from later periods.

O. E. Craig, H. Saul, A. Lucquin, Y. Nishida, K. Taché, L. Clarke, A. Thompson, D. T. Altoft, J. Uchiyama, M. Ajimoto + et al.

doi: 10.1038/nature12109

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Slower recovery in space before collapse of connected populations p.355

Slower recovery from perturbations near a tipping point and its indirect signatures in fluctuation patterns have been suggested to foreshadow catastrophes in a wide variety of systems. Recent studies of populations in the field and in the laboratory have used time-series data to confirm some of the theoretically predicted early warning indicators, such as an increase in recovery time or in the size and timescale of fluctuations. However, the predictive power of temporal warning signals is limited by the demand for long-term observations. Large-scale spatial data are more accessible, but the performance of warning signals in spatially extended systems needs to be examined empirically. Here we use spatially extended yeast populations, an experimental system with a fold bifurcation (tipping point), to evaluate early warning signals based on spatio-temporal fluctuations and to identify a novel spatial warning indicator. We found that two leading indicators based on fluctuations increased before collapse of connected populations; however, the magnitudes of the increases were smaller than those observed in isolated populations, possibly because local variation is reduced by dispersal. Furthermore, we propose a generic indicator based on deterministic spatial patterns, which we call ‘recovery length’. As the spatial counterpart of recovery time, recovery length is the distance necessary for connected populations to recover from spatial perturbations. In our experiments, recovery length increased substantially before population collapse, suggesting that the spatial scale of recovery can provide a superior warning signal before tipping points in spatially extended systems.

Lei Dai, Kirill S. Korolev & Jeff Gore

doi: 10.1038/nature12071

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Rescuing cocaine-induced prefrontal cortex hypoactivity prevents compulsive cocaine seeking p.359

Loss of control over harmful drug seeking is one of the most intractable aspects of addiction, as human substance abusers continue to pursue drugs despite incurring significant negative consequences. Human studies have suggested that deficits in prefrontal cortical function and consequential loss of inhibitory control could be crucial in promoting compulsive drug use. However, it remains unknown whether chronic drug use compromises cortical activity and, equally important, whether this deficit promotes compulsive cocaine seeking. Here we use a rat model of compulsive drug seeking in which cocaine seeking persists in a subgroup of rats despite delivery of noxious foot shocks. We show that prolonged cocaine self-administration decreases ex vivo intrinsic excitability of deep-layer pyramidal neurons in the prelimbic cortex, which was significantly more pronounced in compulsive drug-seeking animals. Furthermore, compensating for hypoactive prelimbic cortex neurons with in vivo optogenetic prelimbic cortex stimulation significantly prevented compulsive cocaine seeking, whereas optogenetic prelimbic cortex inhibition significantly increased compulsive cocaine seeking. Our results show a marked reduction in prelimbic cortex excitability in compulsive cocaine-seeking rats, and that in vivo optogenetic prelimbic cortex stimulation decreased compulsive drug-seeking behaviours. Thus, targeted stimulation of the prefrontal cortex could serve as a promising therapy for treating compulsive drug use.

Billy T. Chen, Hau-Jie Yau, Christina Hatch, Ikue Kusumoto-Yoshida, Saemi L. Cho, F. Woodward Hopf & Antonello Bonci

doi: 10.1038/nature12024

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Visualization of an endogenous retinoic acid gradient across embryonic development p.363

In vertebrate development, the body plan is determined by primordial morphogen gradients that suffuse the embryo. Retinoic acid (RA) is an important morphogen involved in patterning the anterior–posterior axis of structures, including the hindbrain and paraxial mesoderm. RA diffuses over long distances, and its activity is spatially restricted by synthesizing and degrading enzymes. However, gradients of endogenous morphogens in live embryos have not been directly observed; indeed, their existence, distribution and requirement for correct patterning remain controversial. Here we report a family of genetically encoded indicators for RA that we have termed GEPRAs (genetically encoded probes for RA). Using the principle of fluorescence resonance energy transfer we engineered the ligand-binding domains of RA receptors to incorporate cyan-emitting and yellow-emitting fluorescent proteins as fluorescence resonance energy transfer donor and acceptor, respectively, for the reliable detection of ambient free RA. We created three GEPRAs with different affinities for RA, enabling the quantitative measurement of physiological RA concentrations. Live imaging of zebrafish embryos at the gastrula and somitogenesis stages revealed a linear concentration gradient of endogenous RA in a two-tailed source–sink arrangement across the embryo. Modelling of the observed linear RA gradient suggests that the rate of RA diffusion exceeds the spatiotemporal dynamics of embryogenesis, resulting in stability to perturbation. Furthermore, we used GEPRAs in combination with genetic and pharmacological perturbations to resolve competing hypotheses on the structure of the RA gradient during hindbrain formation and somitogenesis. Live imaging of endogenous concentration gradients across embryonic development will allow the precise assignment of molecular mechanisms to developmental dynamics and will accelerate the application of approaches based on morphogen gradients to tissue engineering and regenerative medicine.

Satoshi Shimozono, Tadahiro Iimura, Tetsuya Kitaguchi, Shin-ichi Higashijima & Atsushi Miyawaki

doi: 10.1038/nature12037

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A pathogenic picornavirus acquires an envelope by hijacking cellular membranes p.367

Animal viruses are broadly categorized structurally by the presence or absence of an envelope composed of a lipid-bilayer membrane, attributes that profoundly affect stability, transmission and immune recognition. Among those lacking an envelope, the Picornaviridae are a large and diverse family of positive-strand RNA viruses that includes hepatitis A virus (HAV), an ancient human pathogen that remains a common cause of enterically transmitted hepatitis. HAV infects in a stealth-like manner and replicates efficiently in the liver. Virus-specific antibodies appear only after 3–4 weeks of infection, and typically herald its resolution. Although unexplained mechanistically, both anti-HAV antibody and inactivated whole-virus vaccines prevent disease when administered as late as 2 weeks after exposure, when virus replication is well established in the liver. Here we show that HAV released from cells is cloaked in host-derived membranes, thereby protecting the virion from antibody-mediated neutralization. These enveloped viruses (‘eHAV’) resemble exosomes, small vesicles that are increasingly recognized to be important in intercellular communications. They are fully infectious, sensitive to extraction with chloroform, and circulate in the blood of infected humans. Their biogenesis is dependent on host proteins associated with endosomal-sorting complexes required for transport (ESCRT), namely VPS4B and ALIX. Whereas the hijacking of membranes by HAV facilitates escape from neutralizing antibodies and probably promotes virus spread within the liver, anti-capsid antibodies restrict replication after infection with eHAV, suggesting a possible explanation for prophylaxis after exposure. Membrane hijacking by HAV blurs the classic distinction between ‘enveloped’ and ‘non-enveloped’ viruses and has broad implications for mechanisms of viral egress from infected cells as well as host immune responses.

Zongdi Feng, Lucinda Hensley, Kevin L. McKnight, Fengyu Hu, Victoria Madden, LiFang Ping, Sook-Hyang Jeong, Christopher Walker, Robert E. Lanford & Stanley M. Lemon

doi: 10.1038/nature12029

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Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization p.372

The PARKIN ubiquitin ligase (also known as PARK2) and its regulatory kinase PINK1 (also known as PARK6), often mutated in familial early-onset Parkinson’s disease, have central roles in mitochondrial homeostasis and mitophagy. Whereas PARKIN is recruited to the mitochondrial outer membrane (MOM) upon depolarization via PINK1 action and can ubiquitylate porin, mitofusin and Miro proteins on the MOM, the full repertoire of PARKIN substrates—the PARKIN-dependent ubiquitylome—remains poorly defined. Here we use quantitative diGly capture proteomics (diGly) to elucidate the ubiquitylation site specificity and topology of PARKIN-dependent target modification in response to mitochondrial depolarization. Hundreds of dynamically regulated ubiquitylation sites in dozens of proteins were identified, with strong enrichment for MOM proteins, indicating that PARKIN dramatically alters the ubiquitylation status of the mitochondrial proteome. Using complementary interaction proteomics, we found depolarization-dependent PARKIN association with numerous MOM targets, autophagy receptors, and the proteasome. Mutation of the PARKIN active site residue C431, which has been found mutated in Parkinson’s disease patients, largely disrupts these associations. Structural and topological analysis revealed extensive conservation of PARKIN-dependent ubiquitylation sites on cytoplasmic domains in vertebrate and Drosophila melanogaster MOM proteins. These studies provide a resource for understanding how the PINK1–PARKIN pathway re-sculpts the proteome to support mitochondrial homeostasis.

Shireen A. Sarraf, Malavika Raman, Virginia Guarani-Pereira, Mathew E. Sowa, Edward L. Huttlin, Steven P. Gygi & J. Wade Harper

doi: 10.1038/nature12043

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A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly p.377

A hallmark of histone H3 lysine 9 (H3K9)-methylated heterochromatin, conserved from the fission yeast Schizosaccharomyces pombe to humans, is its ability to spread to adjacent genomic regions. Central to heterochromatin spread is heterochromatin protein 1 (HP1), which recognizes H3K9-methylated chromatin, oligomerizes and forms a versatile platform that participates in diverse nuclear functions, ranging from gene silencing to chromosome segregation. How HP1 proteins assemble on methylated nucleosomal templates and how the HP1–nucleosome complex achieves functional versatility remain poorly understood. Here we show that binding of the key S. pombe HP1 protein, Swi6, to methylated nucleosomes drives a switch from an auto-inhibited state to a spreading-competent state. In the auto-inhibited state, a histone-mimic sequence in one Swi6 monomer blocks methyl-mark recognition by the chromodomain of another monomer. Auto-inhibition is relieved by recognition of two template features, the H3K9 methyl mark and nucleosomal DNA. Cryo-electron-microscopy-based reconstruction of the Swi6–nucleosome complex provides the overall architecture of the spreading-competent state in which two unbound chromodomain sticky ends appear exposed. Disruption of the switch between the auto-inhibited and spreading-competent states disrupts heterochromatin assembly and gene silencing in vivo. These findings are reminiscent of other conditionally activated polymerization processes, such as actin nucleation, and open up a new class of regulatory mechanisms that operate on chromatin in vivo.

Daniele Canzio, Maofu Liao, Nariman Naber, Edward Pate, Adam Larson, Shenping Wu, Diana B. Marina, Jennifer F. Garcia, Hiten D. Madhani, Roger Cooke + et al.

doi: 10.1038/nature12032

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Structural basis of kynurenine 3-monooxygenase inhibition p.382

Inhibition of kynurenine 3-monooxygenase (KMO), an enzyme in the eukaryotic tryptophan catabolic pathway (that is, kynurenine pathway), leads to amelioration of Huntington’s-disease-relevant phenotypes in yeast, fruitfly and mouse models, as well as in a mouse model of Alzheimer’s disease. KMO is a flavin adenine dinucleotide (FAD)-dependent monooxygenase and is located in the outer mitochondrial membrane where it converts l-kynurenine to 3-hydroxykynurenine. Perturbations in the levels of kynurenine pathway metabolites have been linked to the pathogenesis of a spectrum of brain disorders, as well as cancer and several peripheral inflammatory conditions. Despite the importance of KMO as a target for neurodegenerative disease, the molecular basis of KMO inhibition by available lead compounds has remained unknown. Here we report the first crystal structure of Saccharomyces cerevisiae KMO, in the free form and in complex with the tight-binding inhibitor UPF 648. UPF 648 binds close to the FAD cofactor and perturbs the local active-site structure, preventing productive binding of the substrate l-kynurenine. Functional assays and targeted mutagenesis reveal that the active-site architecture and UPF 648 binding are essentially identical in human KMO, validating the yeast KMO–UPF 648 structure as a template for structure-based drug design. This will inform the search for new KMO inhibitors that are able to cross the blood–brain barrier in targeted therapies against neurodegenerative diseases such as Huntington’s, Alzheimer’s and Parkinson’s diseases.

Marta Amaral, Colin Levy, Derren J. Heyes, Pierre Lafite, Tiago F. Outeiro, Flaviano Giorgini, David Leys & Nigel S. Scrutton

doi: 10.1038/nature12039

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