Editorials
日本政府は、女性の社会進出を促すという公約を、しっかり守る必要がある。
Still less equal p.535
Japan’s government must stick by its promise to help women’s careers to prosper.
doi: 10.1038/497535b
Xプライズ財団のコンテストの、DNAシークエンシング技術の推進を目指す意図は高く評価すべきだ。
Overtaken by events p.535
Despite the small number of entries, the genomics X prize is to be commended for attempting to push the boundaries of DNA sequencing technology.
doi: 10.1038/497535a
科学のグローバル化は歓迎すべきことだが、各国国内の科学基盤が置き去りになる恐れがある。
Without borders p.536
Increasing scientific globalization is welcome, but could compromise national efforts.
doi: 10.1038/497536a
News
注目を浴びたヒトクローンES細胞作製の論文に複数の誤りが見つかり、速すぎる論文受理、発表に疑問の声が。
Fallout from hailed cloning paper p.543
Duplicated figures raise debate over expedited publication.
doi: 10.1038/497543a
がんの免疫療法に期待が高まっているが、治療コストも上昇する懸念が。
Immunotherapy’s cancer remit widens p.544
Combination therapies hold great promise, but at what cost?
doi: 10.1038/497544a
北米東部で17年ゼミが大量発生し、その謎の解明に、研究者たちが意気込みを。
Long-lived insects raise prime riddle p.545
Mass orgy of 17-year cicadas sets US researchers buzzing.
doi: 10.1038/497545a
Xプライズ財団のゲノミクスコンテストに参加登録したのは、わずか2チームだけに。
Tepid showing for genomics X prize p.546
Challenge may be too hard and commercially unnecessary.
doi: 10.1038/497546a
安倍政権が、科学改革により経済成長を目指す方針を。
Japan aims high for growth p.548
Innovation in science is at the heart of government plans to boost the economy.
doi: 10.1038/497548a
News Features
神経科学：実験手法の男
Neuroscience: Method man p.550
Karl Deisserothは、先駆的な画像化技術の開発を着実に積み重ねており、脳科学に大きな影響を与えている。
doi: 10.1038/497550a
天文学：宇宙の夜明け
Galaxy formation: Cosmic dawn p.554
ハッブル宇宙望遠鏡によって、初期宇宙での銀河誕生の瞬間が見え始めている。
doi: 10.1038/497554a
News & Views
認知神経科学：時間、空間と記憶
Cognitive neuroscience: Time, space and memory p.568
脳の海馬に含まれる場所細胞は、動物がいる特定の場所を符号化している。海馬のニューロンが時間にも応答する可能性が見いだされたことは、エピソード記憶の符号化に関する手がかりとなるかもしれない。
doi: 10.1038/497568a
ゲノミクス：トウヒのゲノム塩基配列
Genomics: A spruce sequence p.569
裸子植物の全ゲノム概要配列が初めて解読された。これはオウシュウトウヒのゲノムで、裸子植物という大きなグループに固有の分化、適応や進化について研究を進めるための強力な基盤となる。
doi: 10.1038/nature12250
惑星科学：岩石惑星の進化の分かれ目
Planetary science: Evolutionary dichotomy for rocky planets p.570
中心星に近い位置にある岩石惑星は固化が非常にゆっくりなので、水が宇宙空間に失われてしまって乾燥状態になるが、もっと遠くにある惑星は迅速に固化して水を保持していることが、単純なモデルから明らかになった。
doi: 10.1038/497570a
合成生物学：アナログワールド
Synthetic biology: It's an analog world p.572
アナログ計算を使う初めての合成遺伝回路が開発された。このような回路はデジタル計算回路に比べると関係する構成要素とリソースの数が少なく、もっと複雑な操作を実行できる。
doi: 10.1038/nature12246
古人類学：人類史についてためらわれる判断
Palaeoanthropology: Hesitation on hominin history p.573
アウストラロピテクス類に属するAustralopithecus sedibaの化石骨格の詳細な研究から、この初期人類種の解剖学的性質の興味深い詳細が明らかになった。だが、この結果は現生人類への進化の道すじのどこにこの種が位置するのかを確実に示しているわけではない。
doi: 10.1038/497573a
宇宙物理学：マグネターの内部を覗く
Astrophysics: A glimpse inside a magnetar p.574
非常に多くの中性子星で、そのスピンダウン率にグリッチが観測されている。これは星の内部に超高密度の超流動体が存在することを示している。今回、強力な磁場を持つ星で、「逆向き」のグリッチが観測されるという意外な事態が起こった。
doi: 10.1038/497574a
生化学：酵素の後ろ姿
Biochemistry: Rear view of an enzyme p.576
Ubc9酵素は、小型の修飾タンパク質SUMOを標的タンパク質に結合させる反応を仲介する。Ubc9が最適に機能し、細胞が適切に減数分裂を行うには、Ubc9自体がSUMOによって修飾される必要があることが明らかになった。
doi: 10.1038/nature12249
がん：「効く薬が作りにくい」タンパク質を狙い撃ちする薬
Cancer: Drug for an 'undruggable' protein p.577
がん関連タンパク質であるKRASに対する薬剤の開発はずっと以前から試みられてきたが、成功していない。今回、このがんタンパク質の細胞内局在状態を標的とする新規な手法が考案され、この分野の研究が再び活発になりそうだ。
doi: 10.1038/nature12248
Articles
遺伝：オウシュウトウヒのゲノム塩基配列と針葉樹ゲノムの進化
The Norway spruce genome sequence and conifer genome evolution OPEN p.579
The draft genome of the Norway spruce (P. abies) is presented; this is the first gymnosperm genome to be sequenced and reveals a large genome size (20 Gb) resulting from the accumulation of transposable elements, and comparative sequencing of five other gymnosperm genomes provides insights into conifer genome evolution.
doi: 10.1038/nature12211
脳：複雑な認知課題における混合選択性の重要性
The importance of mixed selectivity in complex cognitive tasks p.585
When an animal is performing a cognitive task, individual neurons in the prefrontal cortex show a mixture of responses that is often difficult to decipher and interpret; here new computational methods to decode and extract rich sets of information from these neural responses are revealed and demonstrate how this mixed selectivity offers a computational advantage over specialized cells.
doi: 10.1038/nature12160
Letters
宇宙：マグネターに見つかった反グリッチ
An anti-glitch in a magnetar p.591
Magnetars are neutron stars with X-ray and soft γ-ray outbursts thought to be powered by intense internal magnetic fields. Like conventional neutron stars in the form of radio pulsars, magnetars exhibit ‘glitches’ during which angular momentum is believed to be transferred between the solid outer crust and the superfluid component of the inner crust. The several hundred observed glitches in radio pulsars and magnetars have involved a sudden spin-up (increase in the angular velocity) of the star, presumably because the interior superfluid was rotating faster than the crust. Here we report X-ray timing observations of the magnetar 1E 2259+586 (ref. 8), which exhibited a clear ‘anti-glitch’—a sudden spin-down. We show that this event, like some previous magnetar spin-up glitches, was accompanied by multiple X-ray radiative changes and a significant spin-down rate change. Such behaviour is not predicted by models of neutron star spin-down and, if of internal origin, is suggestive of differential rotation in the magnetar, supporting the need for a rethinking of glitch theory for all neutron stars.
doi: 10.1038/nature12159
物性：グラフェン超格子におけるディラックフェルミオンのクローニング
Cloning of Dirac fermions in graphene superlattices p.594
Superlattices have attracted great interest because their use may make it possible to modify the spectra of two-dimensional electron systems and, ultimately, create materials with tailored electronic properties. In previous studies (see, for example, refs 1, 2, 3, 4, 5, 6, 7, 8), it proved difficult to realize superlattices with short periodicities and weak disorder, and most of their observed features could be explained in terms of cyclotron orbits commensurate with the superlattice. Evidence for the formation of superlattice minibands (forming a fractal spectrum known as Hofstadter’s butterfly) has been limited to the observation of new low-field oscillations and an internal structure within Landau levels. Here we report transport properties of graphene placed on a boron nitride substrate and accurately aligned along its crystallographic directions. The substrate’s moiré potential acts as a superlattice and leads to profound changes in the graphene’s electronic spectrum. Second-generation Dirac points appear as pronounced peaks in resistivity, accompanied by reversal of the Hall effect. The latter indicates that the effective sign of the charge carriers changes within graphene’s conduction and valence bands. Strong magnetic fields lead to Zak-type cloning of the third generation of Dirac points, which are observed as numerous neutrality points in fields where a unit fraction of the flux quantum pierces the superlattice unit cell. Graphene superlattices such as this one provide a way of studying the rich physics expected in incommensurable quantum systems and illustrate the possibility of controllably modifying the electronic spectra of two-dimensional atomic crystals by varying their crystallographic alignment within van der Waals heterostuctures.
doi: 10.1038/nature12187
物性：モアレ超格子における「ホフスタッターの蝶」とフラクタル量子ホール効果
Hofstadter’s butterfly and the fractal quantum Hall effect in moiré superlattices p.598
Electrons moving through a spatially periodic lattice potential develop a quantized energy spectrum consisting of discrete Bloch bands. In two dimensions, electrons moving through a magnetic field also develop a quantized energy spectrum, consisting of highly degenerate Landau energy levels. When subject to both a magnetic field and a periodic electrostatic potential, two-dimensional systems of electrons exhibit a self-similar recursive energy spectrum. Known as Hofstadter’s butterfly, this complex spectrum results from an interplay between the characteristic lengths associated with the two quantizing fields, and is one of the first quantum fractals discovered in physics. In the decades since its prediction, experimental attempts to study this effect have been limited by difficulties in reconciling the two length scales. Typical atomic lattices (with periodicities of less than one nanometre) require unfeasibly large magnetic fields to reach the commensurability condition, and in artificially engineered structures (with periodicities greater than about 100 nanometres) the corresponding fields are too small to overcome disorder completely. Here we demonstrate that moiré superlattices arising in bilayer graphene coupled to hexagonal boron nitride provide a periodic modulation with ideal length scales of the order of ten nanometres, enabling unprecedented experimental access to the fractal spectrum. We confirm that quantum Hall features associated with the fractal gaps are described by two integer topological quantum numbers, and report evidence of their recursive structure. Observation of a Hofstadter spectrum in bilayer graphene means that it is possible to investigate emergent behaviour within a fractal energy landscape in a system with tunable internal degrees of freedom.
doi: 10.1038/nature12186
地球：過去3万5000年にわたる北極海中央部深部からの持続的な231Pa移出
Persistent export of 231Pa from the deep central Arctic Ocean over the past 35,000 years p.603
The Arctic Ocean has an important role in Earth’s climate, both through surface processes such as sea-ice formation and transport, and through the production and export of waters at depth that contribute to the global thermohaline circulation. Deciphering the deep Arctic Ocean’s palaeo-oceanographic history is a crucial part of understanding its role in climatic change. Here we show that sedimentary ratios of the radionuclides thorium-230 (230Th) and protactinium-231 (231Pa), which are produced in sea water and removed by particle scavenging on timescales of decades to centuries, respectively, record consistent evidence for the export of 231Pa from the deep Arctic and may indicate continuous deep-water exchange between the Arctic and Atlantic oceans throughout the past 35,000 years. Seven well-dated box-core records provide a comprehensive overview of 231Pa and 230Th burial in Arctic sediments during glacial, deglacial and interglacial conditions. Sedimentary 231Pa/230Th ratios decrease nearly linearly with increasing water depth above the core sites, indicating efficient particle scavenging in the upper water column and greater influence of removal by lateral transport at depth. Although the measured 230Th burial is in balance with its production in Arctic sea water, integrated depth profiles for all time intervals reveal a deficit in 231Pa burial that can be balanced only by lateral export in the water column. Because no enhanced sink for 231Pa has yet been found in the Arctic, our records suggest that deep-water exchange through the Fram strait may export 231Pa. Such export may have continued for the past 35,000 years, suggesting a century-scale replacement time for deep waters in the Arctic Ocean since the most recent glaciation and a persistent contribution of Arctic waters to the global ocean circulation.
doi: 10.1038/nature12145
地球：マグマオーシャンの固化過程で分類される2つのタイプの地球型惑星
Emergence of two types of terrestrial planet on solidification of magma ocean p.607
Understanding the origins of the diversity in terrestrial planets is a fundamental goal in Earth and planetary sciences. In the Solar System, Venus has a similar size and bulk composition to those of Earth, but it lacks water. Because a richer variety of exoplanets is expected to be discovered, prediction of their atmospheres and surface environments requires a general framework for planetary evolution. Here we show that terrestrial planets can be divided into two distinct types on the basis of their evolutionary history during solidification from the initially hot molten state expected from the standard formation model. Even if, apart from their orbits, they were identical just after formation, the solidified planets can have different characteristics. A type I planet, which is formed beyond a certain critical distance from the host star, solidifies within several million years. If the planet acquires water during formation, most of this water is retained and forms the earliest oceans. In contrast, on a type II planet, which is formed inside the critical distance, a magma ocean can be sustained for longer, even with a larger initial amount of water. Its duration could be as long as 100 million years if the planet is formed together with a mass of water comparable to the total inventory of the modern Earth. Hydrodynamic escape desiccates type II planets during the slow solidification process. Although Earth is categorized as type I, it is not clear which type Venus is because its orbital distance is close to the critical distance. However, because the dryness of the surface and mantle predicted for type II planets is consistent with the characteristics of Venus, it may be representative of type II planets. Also, future observations may have a chance to detect not only terrestrial exoplanets covered with water ocean but also those covered with magma ocean around a young star.
doi: 10.1038/nature12163
進化：旧世界ザルと類人猿が漸新世に分岐したことを示す古生物学的証拠
Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes p.611
Apes and Old World monkeys are prominent components of modern African and Asian ecosystems, yet the earliest phases of their evolutionary history have remained largely undocumented. The absence of crown catarrhine fossils older than ∼20 million years (Myr) has stood in stark contrast to molecular divergence estimates of ∼25–30 Myr for the split between Cercopithecoidea (Old World monkeys) and Hominoidea (apes), implying long ghost lineages for both clades. Here we describe the oldest known fossil ‘ape’, represented by a partial mandible preserving dental features that place it with ‘nyanzapithecine’ stem hominoids. Additionally, we report the oldest stem member of the Old World monkey clade, represented by a lower third molar. Both specimens were recovered from a precisely dated 25.2-Myr-old stratum in the Rukwa Rift, a segment of the western branch of the East African Rift in Tanzania. These finds extend the fossil record of apes and Old World monkeys well into the Oligocene epoch of Africa, suggesting a possible link between diversification of crown catarrhines and changes in the African landscape brought about by previously unrecognized tectonic activity in the East African rift system.
doi: 10.1038/nature12161
生態：長期的な温暖化は北極域で正味の土壌炭素貯蔵量を変化させずにツンドラを再編成する
Long-term warming restructures Arctic tundra without changing net soil carbon storage p.615
High latitudes contain nearly half of global soil carbon, prompting interest in understanding how the Arctic terrestrial carbon balance will respond to rising temperatures. Low temperatures suppress the activity of soil biota, retarding decomposition and nitrogen release, which limits plant and microbial growth. Warming initially accelerates decomposition, increasing nitrogen availability, productivity and woody-plant dominance. However, these responses may be transitory, because coupled abiotic–biotic feedback loops that alter soil-temperature dynamics and change the structure and activity of soil communities, can develop. Here we report the results of a two-decade summer warming experiment in an Alaskan tundra ecosystem. Warming increased plant biomass and woody dominance, indirectly increased winter soil temperature, homogenized the soil trophic structure across horizons and suppressed surface-soil-decomposer activity, but did not change total soil carbon or nitrogen stocks, thereby increasing net ecosystem carbon storage. Notably, the strongest effects were in the mineral horizon, where warming increased decomposer activity and carbon stock: a ‘biotic awakening’ at depth.
doi: 10.1038/nature12129
合成生物学：生きている細胞における合成アナログ演算
Synthetic analog computation in living cells p.619
A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber’s law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.
doi: 10.1038/nature12148
細胞：BAF複合体はトポイソメラーゼIIαによるDNAのデカテネーションを促進する
BAF complexes facilitate decatenation of DNA by topoisomerase IIα p.624
Recent exon-sequencing studies of human tumours have revealed that subunits of BAF (mammalian SWI/SNF) complexes are mutated in more than 20% of all human malignancies, but the mechanisms involved in tumour suppression are unclear. BAF chromatin-remodelling complexes are polymorphic assemblies that use energy provided by ATP hydrolysis to regulate transcription through the control of chromatin structure and the placement of Polycomb repressive complex 2 (PRC2) across the genome. Several proteins dedicated to this multisubunit complex, including BRG1 (also known as SMARCA4) and BAF250a (also known as ARID1A), are mutated at frequencies similar to those of recognized tumour suppressors. In particular, the core ATPase BRG1 is mutated in 5–10% of childhood medulloblastomas and more than 15% of Burkitt’s lymphomas. Here we show a previously unknown function of BAF complexes in decatenating newly replicated sister chromatids, a requirement for proper chromosome segregation during mitosis. We find that deletion of Brg1 in mouse cells, as well as the expression of BRG1 point mutants identified in human tumours, leads to anaphase bridge formation (in which sister chromatids are linked by catenated strands of DNA) and a G2/M-phase block characteristic of the decatenation checkpoint. Endogenous BAF complexes interact directly with endogenous topoisomerase IIα (TOP2A) through BAF250a and are required for the binding of TOP2A to approximately 12,000 sites across the genome. Our results demonstrate that TOP2A chromatin binding is dependent on the ATPase activity of BRG1, which is compromised in oncogenic BRG1 mutants. These studies indicate that the ability of TOP2A to prevent DNA entanglement at mitosis requires BAF complexes and suggest that this activity contributes to the role of BAF subunits as tumour suppressors.
doi: 10.1038/nature12146
細胞：脊椎動物組織のパターン形成の際には、特殊化した糸状仮足がSHHの長距離輸送を行う
Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning p.628
The ability of signalling proteins to traverse tissues containing tightly packed cells is of fundamental importance for cell specification and tissue development; however, how this is achieved at a cellular level remains poorly understood. For more than a century, the vertebrate limb bud has served as a model for studying cell signalling during embryonic development. Here we optimize single-cell real-time imaging to delineate the cellular mechanisms for how signalling proteins, such as sonic hedgehog (SHH), that possess membrane-bound covalent lipid modifications traverse long distances within the vertebrate limb bud in vivo. By directly imaging SHH ligand production under native regulatory control in chick (Gallus gallus) embryos, our findings show that SHH is unexpectedly produced in the form of a particle that remains associated with the cell via long cytoplasmic extensions that span several cell diameters. We show that these cellular extensions are a specialized class of actin-based filopodia with novel cytoskeletal features that have not been previously described. Notably, particles containing SHH travel along these extensions with a net anterograde movement within the field of SHH cell signalling. We further show that in SHH-responding cells, specific subsets of SHH co-receptors, including cell adhesion molecule downregulated by oncogenes (CDO) and brother of CDO (BOC), actively distribute and co-localize in specific micro-domains within filopodial extensions, far from the cell body. Stabilized interactions are formed between filopodia containing SHH ligand and those containing co-receptors over a long range. These results suggest that contact-mediated release propagated by specialized filopodia contributes to the delivery of SHH at a distance. Together, these studies identify an important mode of communication between cells that considerably extends our understanding of ligand movement and reception during vertebrate tissue patterning.
doi: 10.1038/nature12157
細胞：タンパク質のマクロピノサイトーシスはRas形質転換細胞におけるアミノ酸供給経路である
Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells p.633
Macropinocytosis is a highly conserved endocytic process by which extracellular fluid and its contents are internalized into cells through large, heterogeneous vesicles known as macropinosomes. Oncogenic Ras proteins have been shown to stimulate macropinocytosis but the functional contribution of this uptake mechanism to the transformed phenotype remains unknown. Here we show that Ras-transformed cells use macropinocytosis to transport extracellular protein into the cell. The internalized protein undergoes proteolytic degradation, yielding amino acids including glutamine that can enter central carbon metabolism. Accordingly, the dependence of Ras-transformed cells on free extracellular glutamine for growth can be suppressed by the macropinocytic uptake of protein. Consistent with macropinocytosis representing an important route of nutrient uptake in tumours, its pharmacological inhibition compromises the growth of Ras-transformed pancreatic tumour xenografts. These results identify macropinocytosis as a mechanism by which cancer cells support their unique metabolic needs and point to the possible exploitation of this process in the design of anticancer therapies.
doi: 10.1038/nature12138
がん：KRAS–PDEδ相互作用の低分子化合物による阻害は発がん性のKRASシグナル伝達を障害する
Small molecule inhibition of the KRAS–PDEδ interaction impairs oncogenic KRAS signalling p.638
The KRAS oncogene product is considered a major target in anticancer drug discovery. However, direct interference with KRAS signalling has not yet led to clinically useful drugs. Correct localization and signalling by farnesylated KRAS is regulated by the prenyl-binding protein PDEδ, which sustains the spatial organization of KRAS by facilitating its diffusion in the cytoplasm. Here we report that interfering with binding of mammalian PDEδ to KRAS by means of small molecules provides a novel opportunity to suppress oncogenic RAS signalling by altering its localization to endomembranes. Biochemical screening and subsequent structure-based hit optimization yielded inhibitors of the KRAS–PDEδ interaction that selectively bind to the prenyl-binding pocket of PDEδ with nanomolar affinity, inhibit oncogenic RAS signalling and suppress in vitro and in vivo proliferation of human pancreatic ductal adenocarcinoma cells that are dependent on oncogenic KRAS. Our findings may inspire novel drug discovery efforts aimed at the development of drugs targeting oncogenic RAS.
doi: 10.1038/nature12205
医学：低温電子顕微鏡法と全原子分子動力学法による成熟HIV-1キャプシドの構造
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics p.643
Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a ‘fullerene cone’ model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
doi: 10.1038/nature12162
生化学：硝酸塩/亜硝酸塩交換輸送体の結晶構造
Crystal structure of a nitrate/nitrite exchanger p.647
Mineral nitrogen in nature is often found in the form of nitrate (NO3−). Numerous microorganisms evolved to assimilate nitrate and use it as a major source of mineral nitrogen uptake. Nitrate, which is central in nitrogen metabolism, is first reduced to nitrite (NO2−) through a two-electron reduction reaction. The accumulation of cellular nitrite can be harmful because nitrite can be reduced to the cytotoxic nitric oxide. Instead, nitrite is rapidly removed from the cell by channels and transporters, or reduced to ammonium or dinitrogen through the action of assimilatory enzymes. Despite decades of effort no structure is currently available for any nitrate transport protein and the mechanism by which nitrate is transported remains largely unknown. Here we report the structure of a bacterial nitrate/nitrite transport protein, NarK, from Escherichia coli, with and without substrate. The structures reveal a positively charged substrate-translocation pathway lacking protonatable residues, suggesting that NarK functions as a nitrate/nitrite exchanger and that protons are unlikely to be co-transported. Conserved arginine residues comprise the substrate-binding pocket, which is formed by association of helices from the two halves of NarK. Key residues that are important for substrate recognition and transport are identified and related to extensive mutagenesis and functional studies. We propose that NarK exchanges nitrate for nitrite by a rocker switch mechanism facilitated by inter-domain hydrogen bond networks.
doi: 10.1038/nature12139
