Nature

Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.
  • Dynamically important magnetic fields near accreting supermassive black holes
    [Jun 2014]

    Dynamically important magnetic fields near accreting supermassive black holes

    Nature 510, 7503 (2014). doi:10.1038/nature13399

    Authors: M. Zamaninasab, E. Clausen-Brown, T. Savolainen & A. Tchekhovskoy

    Accreting supermassive black holes at the centres of active galaxies often produce ‘jets’—collimated bipolar outflows of relativistic particles. Magnetic fields probably play a critical role in jet formation and in accretion disk physics. A dynamically important magnetic field was recently found near the Galactic Centre black hole. If this is common and if the field continues to near the black hole event horizon, disk structures will be affected, invalidating assumptions made in standard models. Here we report that jet magnetic field and accretion disk luminosity are tightly correlated over seven orders of magnitude for a sample of 76 radio-loud active galaxies. We conclude that the jet-launching regions of these radio-loud galaxies are threaded by dynamically important fields, which will affect the disk properties. These fields obstruct gas infall, compress the accretion disk vertically, slow down the disk rotation by carrying away its angular momentum in an outflow and determine the directionality of jets.

    Categories: Journal Articles
  • Ubiquitin is phosphorylated by PINK1 to activate parkin
    [Jun 2014]

    Ubiquitin is phosphorylated by PINK1 to activate parkin

    Nature 510, 7503 (2014). doi:10.1038/nature13392

    Authors: Fumika Koyano, Kei Okatsu, Hidetaka Kosako, Yasushi Tamura, Etsu Go, Mayumi Kimura, Yoko Kimura, Hikaru Tsuchiya, Hidehito Yoshihara, Takatsugu Hirokawa, Toshiya Endo, Edward A. Fon, Jean-François Trempe, Yasushi Saeki, Keiji Tanaka & Noriyuki Matsuda

    PINK1 (PTEN induced putative kinase 1) and PARKIN (also known as PARK2) have been identified as the causal genes responsible for hereditary recessive early-onset Parkinsonism. PINK1 is a Ser/Thr kinase that specifically accumulates on depolarized mitochondria, whereas parkin is an E3 ubiquitin ligase that catalyses ubiquitin transfer to mitochondrial substrates. PINK1 acts as an upstream factor for parkin and is essential both for the activation of latent E3 parkin activity and for recruiting parkin onto depolarized mitochondria. Recently, mechanistic insights into mitochondrial quality control mediated by PINK1 and parkin have been revealed, and PINK1-dependent phosphorylation of parkin has been reported. However, the requirement of PINK1 for parkin activation was not bypassed by phosphomimetic parkin mutation, and how PINK1 accelerates the E3 activity of parkin on damaged mitochondria is still obscure. Here we report that ubiquitin is the genuine substrate of PINK1. PINK1 phosphorylated ubiquitin at Ser 65 both in vitro and in cells, and a Ser 65 phosphopeptide derived from endogenous ubiquitin was only detected in cells in the presence of PINK1 and following a decrease in mitochondrial membrane potential. Unexpectedly, phosphomimetic ubiquitin bypassed PINK1-dependent activation of a phosphomimetic parkin mutant in cells. Furthermore, phosphomimetic ubiquitin accelerates discharge of the thioester conjugate formed by UBCH7 (also known as UBE2L3) and ubiquitin (UBCH7∼ubiquitin) in the presence of parkin in vitro, indicating that it acts allosterically. The phosphorylation-dependent interaction between ubiquitin and parkin suggests that phosphorylated ubiquitin unlocks autoinhibition of the catalytic cysteine. Our results show that PINK1-dependent phosphorylation of both parkin and ubiquitin is sufficient for full activation of parkin E3 activity. These findings demonstrate that phosphorylated ubiquitin is a parkin activator.

    Categories: Journal Articles
  • Membrane proteins bind lipids selectively to modulate their structure and function
    [Jun 2014]

    Membrane proteins bind lipids selectively to modulate their structure and function

    Nature 510, 7503 (2014). doi:10.1038/nature13419

    Authors: Arthur Laganowsky, Eamonn Reading, Timothy M. Allison, Martin B. Ulmschneider, Matteo T. Degiacomi, Andrew J. Baldwin & Carol V. Robinson

    Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding.

    Categories: Journal Articles
  • Corrigendum: Realizing the promise of cancer predisposition genes
    [Jun 2014]

    Corrigendum: Realizing the promise of cancer predisposition genes

    Nature 510, 7503 (2014). doi:10.1038/nature13431

    Author: Nazneen Rahman

    Nature505, 302–308 (2014); doi:10.1038/nature12981In Figure 1 of this Article, the gene RET was incorrectly repeated on chromosome 12 and the genes BRIP1 and TRIM37 were omitted from chromosome 17. We thank Eric Song from

    Categories: Journal Articles
  • Big Bang blunder bursts the multiverse bubble
    [Jun 2014]

    Big Bang blunder bursts the multiverse bubble

    Nature 510, 7503 (2014). http://www.nature.com/doifinder/10.1038/510009a

    Author: Paul Steinhardt

    Premature hype over gravitational waves highlights gaping holes in models for the origins and evolution of the Universe, argues Paul Steinhardt.

    Categories: Journal Articles
  • Phage therapy gets revitalized
    [Jun 2014]

    Phage therapy gets revitalized

    Nature 510, 7503 (2014). http://www.nature.com/doifinder/10.1038/510015a

    Author: Sara Reardon

    The rise of antibiotic resistance rekindles interest in a century-old virus treatment.

    Categories: Journal Articles
  • Funding windfall rescues abandoned stem-cell trial
    [Jun 2014]

    Funding windfall rescues abandoned stem-cell trial

    Nature 510, 7503 (2014). http://www.nature.com/doifinder/10.1038/510018a

    Author: Erika Check Hayden

    But more players have joined the quest to treat spinal-cord injury with embryonic cells.

    Categories: Journal Articles
  • Big Bang finding challenged
    [Jun 2014]

    Big Bang finding challenged

    Nature 510, 7503 (2014). http://www.nature.com/doifinder/10.1038/510020a

    Author: Ron Cowan

    Signal of gravitational waves was too weak to be significant, studies suggest.

    Categories: Journal Articles
  • Climate science: How Antarctic ice retreats
    [May 2014]

    Climate science: How Antarctic ice retreats

    Nature 510, 7503 (2014). doi:10.1038/nature13345

    Authors: Trevor Williams

    New records of iceberg-rafted debris from the Scotia Sea reveal episodic retreat of the Antarctic Ice Sheet since the peak of the last glacial period, in step with changes in climate and global sea level. See Letter p.134

    Categories: Journal Articles
  • Palladium-catalysed C–H activation of aliphatic amines to give strained nitrogen heterocycles
    [May 2014]

    Palladium-catalysed C–H activation of aliphatic amines to give strained nitrogen heterocycles

    Nature 510, 7503 (2014). doi:10.1038/nature13389

    Authors: Andrew McNally, Benjamin Haffemayer, Beatrice S. L. Collins & Matthew J. Gaunt

    The development of new chemical transformations based on catalytic functionalization of unactivated C−H bonds has the potential to simplify the synthesis of complex molecules dramatically. Transition metal catalysis has emerged as a powerful tool with which to convert these unreactive bonds into carbon−carbon and carbon−heteroatom bonds, but the selective transformation of aliphatic C−H bonds is still a challenge. The most successful approaches involve a ‘directing group’, which positions the metal catalyst near a particular C−H bond, so that the C−H functionalization step occurs via cyclometallation. Most directed aliphatic C−H activation processes proceed through a five-membered-ring cyclometallated intermediate. Considering the number of new reactions that have arisen from such intermediates, it seems likely that identification of distinct cyclometallation pathways would lead to the development of other useful chemical transformations. Here we report a palladium-catalysed C−H bond activation mode that proceeds through a four-membered-ring cyclopalladation pathway. The chemistry described here leads to the selective transformation of a methyl group that is adjacent to an unprotected secondary amine into a synthetically versatile nitrogen heterocycle. The scope of this previously unknown bond disconnection is highlighted through the development of C−H amination and carbonylation processes, leading to the synthesis of aziridines and β-lactams (respectively), and is suggestive of a generic C−H functionalization platform that could simplify the synthesis of aliphatic secondary amines, a class of small molecules that are particularly important features of many pharmaceutical agents.

    Categories: Journal Articles
  • Millennial-scale variability in Antarctic ice-sheet discharge during the last deglaciation
    [May 2014]

    Millennial-scale variability in Antarctic ice-sheet discharge during the last deglaciation

    Nature 510, 7503 (2014). doi:10.1038/nature13397

    Authors: M. E. Weber, P. U. Clark, G. Kuhn, A. Timmermann, D. Sprenk, R. Gladstone, X. Zhang, G. Lohmann, L. Menviel, M. O. Chikamoto, T. Friedrich & C. Ohlwein

    Our understanding of the deglacial evolution of the Antarctic Ice Sheet (AIS) following the Last Glacial Maximum (26,000–19,000 years ago) is based largely on a few well-dated but temporally and geographically restricted terrestrial and shallow-marine sequences. This sparseness limits our understanding of the dominant feedbacks between the AIS, Southern Hemisphere climate and global sea level. Marine records of iceberg-rafted debris (IBRD) provide a nearly continuous signal of ice-sheet dynamics and variability. IBRD records from the North Atlantic Ocean have been widely used to reconstruct variability in Northern Hemisphere ice sheets, but comparable records from the Southern Ocean of the AIS are lacking because of the low resolution and large dating uncertainties in existing sediment cores. Here we present two well-dated, high-resolution IBRD records that capture a spatially integrated signal of AIS variability during the last deglaciation. We document eight events of increased iceberg flux from various parts of the AIS between 20,000 and 9,000 years ago, in marked contrast to previous scenarios which identified the main AIS retreat as occurring after meltwater pulse 1A and continuing into the late Holocene epoch. The highest IBRD flux occurred 14,600 years ago, providing the first direct evidence for an Antarctic contribution to meltwater pulse 1A. Climate model simulations with AIS freshwater forcing identify a positive feedback between poleward transport of Circumpolar Deep Water, subsurface warming and AIS melt, suggesting that small perturbations to the ice sheet can be substantially enhanced, providing a possible mechanism for rapid sea-level rise.

    Categories: Journal Articles
  • Accurate design of co-assembling multi-component protein nanomaterials
    [May 2014]

    Accurate design of co-assembling multi-component protein nanomaterials

    Nature 510, 7503 (2014). doi:10.1038/nature13404

    Authors: Neil P. King, Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates & David Baker

    The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an

    Categories: Journal Articles
  • Evolutionary biology: Excitation over jelly nerves
    [May 2014]

    Evolutionary biology: Excitation over jelly nerves

    Nature 510, 7503 (2014). doi:10.1038/nature13340

    Authors: Andreas Hejnol

    Analysis of the draft genome of a comb jelly and of gene-transcription profiles from ten other ctenophores hints at an independent evolutionary origin for the nervous systems of these organisms. See Article p.109

    Categories: Journal Articles
  • The ctenophore genome and the evolutionary origins of neural systems
    [May 2014]

    The ctenophore genome and the evolutionary origins of neural systems

    Nature 510, 7503 (2014). doi:10.1038/nature13400

    Authors: Leonid L. Moroz, Kevin M. Kocot, Mathew R. Citarella, Sohn Dosung, Tigran P. Norekian, Inna S. Povolotskaya, Anastasia P. Grigorenko, Christopher Dailey, Eugene Berezikov, Katherine M. Buckley, Andrey Ptitsyn, Denis Reshetov, Krishanu Mukherjee, Tatiana P. Moroz, Yelena Bobkova, Fahong Yu, Vladimir V. Kapitonov, Jerzy Jurka, Yuri V. Bobkov, Joshua J. Swore, David O. Girardo, Alexander Fodor, Fedor Gusev, Rachel Sanford, Rebecca Bruders, Ellen Kittler, Claudia E. Mills, Jonathan P. Rast, Romain Derelle, Victor V. Solovyev, Fyodor A. Kondrashov, Billie J. Swalla, Jonathan V. Sweedler, Evgeny I. Rogaev, Kenneth M. Halanych & Andrea B. Kohn

    The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei

    Categories: Journal Articles
  • Crystal structure of the human glucose transporter GLUT1
    [May 2014]

    Crystal structure of the human glucose transporter GLUT1

    Nature 510, 7503 (2014). doi:10.1038/nature13306

    Authors: Dong Deng, Chao Xu, Pengcheng Sun, Jianping Wu, Chuangye Yan, Mingxu Hu & Nieng Yan

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation,

    Categories: Journal Articles
  • Erratum: Recent advances in homogeneous nickel catalysis
    [May 2014]

    Erratum: Recent advances in homogeneous nickel catalysis

    Nature 510, 7503 (2014). doi:10.1038/nature13463

    Authors: Sarah Z. Tasker, Eric A. Standley & Timothy F. Jamison

    Nature509, 299–309 (2014); doi:10.1038/nature13274In the first paragraph of this Review, the words ‘such as facile oxidative addition and ready access to multiple oxidation states’ were inadvertently repeated in the print version. The paper is correct online.

    Categories: Journal Articles
  • Increasing CO2 threatens human nutrition
    [May 2014]

    Increasing CO2 threatens human nutrition

    Nature 510, 7503 (2014). doi:10.1038/nature13179

    Authors: Samuel S. Myers, Antonella Zanobetti, Itai Kloog, Peter Huybers, Andrew D. B. Leakey, Arnold J. Bloom, Eli Carlisle, Lee H. Dietterich, Glenn Fitzgerald, Toshihiro Hasegawa, N. Michele Holbrook, Randall L. Nelson, Michael J. Ottman, Victor Raboy, Hidemitsu Sakai, Karla A. Sartor, Joel Schwartz, Saman Seneweera, Michael Tausz & Yasuhiro Usui

    Dietary deficiencies of zinc and iron are a substantial global public health problem. An estimated two billion people suffer these deficiencies, causing a loss of 63 million life-years annually. Most of these people depend on C3 grains and legumes as their primary dietary source of zinc and iron. Here we report that C3 grains and legumes have lower concentrations of zinc and iron when grown under field conditions at the elevated atmospheric CO2 concentration predicted for the middle of this century. C3 crops other than legumes also have lower concentrations of protein, whereas C4 crops seem to be less affected. Differences between cultivars of a single crop suggest that breeding for decreased sensitivity to atmospheric CO2 concentration could partly address these new challenges to global health.

    Categories: Journal Articles