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Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system 期刊论文
NATURE, 2020, 577 (7789) : 271-+
作者:  Halpin-Healy, Tyler S.;  Klompe, Sanne E.;  Sternberg, Samuel H.;  Fernandez, Israel S.
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/03

Bacteria use adaptive immune systems encoded by CRISPR and Cas genes to maintain genomic integrity when challenged by pathogens and mobile genetic elements(1-3). Type I CRISPR-Cas systems typically target foreign DNA for degradation via joint action of the ribonucleoprotein complex Cascade and the helicase-nuclease Cas3(4,5), but nuclease-deficient type I systems lacking Cas3 have been repurposed for RNA-guided transposition by bacterial Tn7-like transposons(6,7). How CRISPR- and transposon-associated machineries collaborate during DNA targeting and insertion remains unknown. Here we describe structures of a TniQ-Cascade complex encoded by the Vibrio cholerae Tn6677 transposon using cryo-electron microscopy, revealing the mechanistic basis of this functional coupling. The cryo-electron microscopy maps enabled de novo modelling and refinement of the transposition protein TniQ, which binds to the Cascade complex as a dimer in a head-to-tail configuration, at the interface formed by Cas6 and Cas7 near the 3'  end of the CRISPR RNA (crRNA). The natural Cas8-Cas5 fusion protein binds the 5'  crRNA handle and contacts the TniQ dimer via a flexible insertion domain. A target DNA-bound structure reveals critical interactions necessary for protospacer-adjacent motif recognition and R-loop formation. This work lays the foundation for a structural understanding of how DNA targeting by TniQ-Cascade leads to downstream recruitment of additional transposase proteins, and will guide protein engineering efforts to leverage this system for programmable DNA insertions in genome-engineering applications.


  
Field-resolved infrared spectroscopy of biological systems 期刊论文
NATURE, 2020, 577 (7788) : 52-+
作者:  Pupeza, Ioachim;  Huber, Marinus;  Trubetskov, Michael;  Schweinberger, Wolfgang;  Hussain, Syed A.;  Hofer, Christina;  Fritsch, Kilian;  Poetzlberger, Markus;  Vamos, Lenard;  Fill, Ernst;  Amotchkina, Tatiana;  Kepesidis, Kosmas V.;  Apolonski, Alexander;  Karpowicz, Nicholas;  Pervak, Vladimir;  Pronin, Oleg;  Fleischmann, Frank;  Azzeer, Abdallah;  Zigman, Mihaela;  Krausz, Ferenc
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

The proper functioning of living systems and physiological phenotypes depends on molecular composition. Yet simultaneous quantitative detection of a wide variety of molecules remains a challenge(1-8). Here we show how broadband optical coherence opens up opportunities for fingerprinting complex molecular ensembles in their natural environment. Vibrationally excited molecules emit a coherent electric field following few-cycle infrared laser excitation(9-12), and this field is specific to the sample'  s molecular composition. Employing electro-optic sampling(10,12-15), we directly measure this global molecular fingerprint down to field strengths 10(7) times weaker than that of the excitation. This enables transillumination of intact living systems with thicknesses of the order of 0.1 millimetres, permitting broadband infrared spectroscopic probing of human cells and plant leaves. In a proof-of-concept analysis of human blood serum, temporal isolation of the infrared electric-field fingerprint from its excitation along with its sampling with attosecond timing precision results in detection sensitivity of submicrograms per millilitre of blood serum and a detectable dynamic range of molecular concentration exceeding 10(5). This technique promises improved molecular sensitivity and molecular coverage for probing complex, real-world biological and medical settings.


  
Molecular basis of beta-arrestin coupling to formoterol-bound beta(1)-adrenoceptor 期刊论文
NATURE, 2020
作者:  Pulliainen, Jouni;  Luojus, Kari;  Derksen, Chris;  Mudryk, Lawrence;  Lemmetyinen, Juha;  Salminen, Miia;  Ikonen, Jaakko;  Takala, Matias;  Cohen, Juval;  Smolander, Tuomo;  Norberg, Johannes
收藏  |  浏览/下载:29/0  |  提交时间:2020/07/03

The beta(1)-adrenoceptor (beta(1)AR) is a G-protein-coupled receptor (GPCR) that couples(1)to the heterotrimeric G protein G(s). G-protein-mediated signalling is terminated by phosphorylation of the C terminus of the receptor by GPCR kinases (GRKs) and by coupling of beta-arrestin 1 (beta arr1, also known as arrestin 2), which displaces G(s)and induces signalling through the MAP kinase pathway(2). The ability of synthetic agonists to induce signalling preferentially through either G proteins or arrestins-known as biased agonism(3)-is important in drug development, because the therapeutic effect may arise from only one signalling cascade, whereas the other pathway may mediate undesirable side effects(4). To understand the molecular basis for arrestin coupling, here we determined the cryo-electron microscopy structure of the beta(1)AR-beta arr1 complex in lipid nanodiscs bound to the biased agonist formoterol(5), and the crystal structure of formoterol-bound beta(1)AR coupled to the G-protein-mimetic nanobody(6)Nb80. beta arr1 couples to beta(1)AR in a manner distinct to that(7)of G(s)coupling to beta(2)AR-the finger loop of beta arr1 occupies a narrower cleft on the intracellular surface, and is closer to transmembrane helix H7 of the receptor when compared with the C-terminal alpha 5 helix of G(s). The conformation of the finger loop in beta arr1 is different from that adopted by the finger loop of visual arrestin when it couples to rhodopsin(8). beta(1)AR coupled to beta arr1 shows considerable differences in structure compared with beta(1)AR coupled to Nb80, including an inward movement of extracellular loop 3 and the cytoplasmic ends of H5 and H6. We observe weakened interactions between formoterol and two serine residues in H5 at the orthosteric binding site of beta(1)AR, and find that formoterol has a lower affinity for the beta(1)AR-beta arr1 complex than for the beta(1)AR-G(s)complex. The structural differences between these complexes of beta(1)AR provide a foundation for the design of small molecules that could bias signalling in the beta-adrenoceptors.


A cryo-electron microscopy structure of the beta 1-adrenoceptor coupled to beta-arrestin 1 and activated by the biased agonist formoterol, as well as the crystal structure of a related formoterol-bound adrenoreceptor, provide insights into biased signalling in these systems.


  
Enhanced ferroelectricity in ultrathin films grown directly on silicon 期刊论文
NATURE, 2020, 580 (7804) : 478-+
作者:  Arnold, Fabian M.;  Weber, Miriam S.;  Gonda, Imre;  Gallenito, Marc J.;  Adenau, Sophia;  Egloff, Pascal;  Zimmermann, Iwan;  Hutter, Cedric A. J.;  Huerlimann, Lea M.;  Peters, Eike E.;  Piel, Joern;  Meloni, Gabriele;  Medalia, Ohad;  Seeger, Markus A.
收藏  |  浏览/下载:49/0  |  提交时间:2020/07/03

Ultrathin ferroelectric materials could potentially enable low-power perovskite ferroelectric tetragonality logic and nonvolatile memories(1,2). As ferroelectric materials are made thinner, however, the ferroelectricity is usually suppressed. Size effects in ferroelectrics have been thoroughly investigated in perovskite oxides-the archetypal ferroelectric system(3). Perovskites, however, have so far proved unsuitable for thickness scaling and integration with modern semiconductor processes(4). Here we report ferroelectricity in ultrathin doped hafnium oxide (HfO2), a fluorite-structure oxide grown by atomic layer deposition on silicon. We demonstrate the persistence of inversion symmetry breaking and spontaneous, switchable polarization down to a thickness of one nanometre. Our results indicate not only the absence of a ferroelectric critical thickness but also enhanced polar distortions as film thickness is reduced, unlike in perovskite ferroelectrics. This approach to enhancing ferroelectricity in ultrathin layers could provide a route towards polarization-driven memories and ferroelectric-based advanced transistors. This work shifts the search for the fundamental limits of ferroelectricity to simpler transition-metal oxide systems-that is, from perovskite-derived complex oxides to fluorite-structure binary oxides-in which '  reverse'  size effects counterintuitively stabilize polar symmetry in the ultrathin regime.


Enhanced switchable ferroelectric polarization is achieved in doped hafnium oxide films grown directly onto silicon using low-temperature atomic layer deposition, even at thicknesses of just one nanometre.


  
Ionic solids from common colloids 期刊论文
NATURE, 2020, 580 (7804) : 487-+
作者:  Delord, T.;  Huillery, P.;  Nicolas, L.;  Hetet, G.
收藏  |  浏览/下载:6/0  |  提交时间:2020/07/03

Oppositely charged colloidal particles are assembled in water through an approach that allows electrostatic interactions to be precisely tuned to generate macroscopic single crystals.


From rock salt to nanoparticle superlattices, complex structure can emerge from simple building blocks that attract each other through Coulombic forces(1-4). On the micrometre scale, however, colloids in water defy the intuitively simple idea of forming crystals from oppositely charged partners, instead forming non-equilibrium structures such as clusters and gels(5-7). Although various systems have been engineered to grow binary crystals(8-11), native surface charge in aqueous conditions has not been used to assemble crystalline materials. Here we form ionic colloidal crystals in water through an approach that we refer to as polymer-attenuated Coulombic self-assembly. The key to crystallization is the use of a neutral polymer to keep particles separated by well defined distances, allowing us to tune the attractive overlap of electrical double layers, directing particles to disperse, crystallize or become permanently fixed on demand. The nucleation and growth of macroscopic single crystals is demonstrated by using the Debye screening length to fine-tune assembly. Using a variety of colloidal particles and commercial polymers, ionic colloidal crystals isostructural to caesium chloride, sodium chloride, aluminium diboride and K4C60 are selected according to particle size ratios. Once fixed by simply diluting out solution salts, crystals are pulled out of the water for further manipulation, demonstrating an accurate translation from solution-phase assembly to dried solid structures. In contrast to other assembly approaches, in which particles must be carefully engineered to encode binding information(12-18), polymer-attenuated Coulombic self-assembly enables conventional colloids to be used as model colloidal ions, primed for crystallization.


  
Construction of a human cell landscape at single-cell level 期刊论文
NATURE, 2020, 581 (7808) : 303-+
作者:  Han, Yan;  Reyes, Alexis A.;  Malik, Sara;  He, Yuan
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex systems(1). However, a comprehensive single-cell atlas has not been achieved for humans. Here we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL). We have uncovered a single-cell hierarchy for many tissues that have not been well characterized. We established a '  single-cell HCL analysis'  pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from human and mouse to identify conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, whereas differentiated cells are more distinct. Our results provide a useful resource for the study of human biology.


Single-cell RNA sequencing is used to generate a dataset covering all major human organs in both adult and fetal stages, enabling comparison with similar datasets for mouse tissues.


  
Constraint on the matter-antimatter symmetry-violating phase in neutrino oscillations 期刊论文
NATURE, 2020, 580 (7803) : 339-+
作者:  Houben, Lothar;  Weissman, Haim;  Wolf, Sharon G.;  Rybtchinski, Boris
收藏  |  浏览/下载:16/0  |  提交时间:2020/07/03

The charge-conjugation and parity-reversal (CP) symmetry of fundamental particles is a symmetry between matter and antimatter. Violation of this CP symmetry was first observed in 1964(1), and CP violation in the weak interactions of quarks was soon established(2). Sakharov proposed(3) that CP violation is necessary to explain the observed imbalance of matter and antimatter abundance in the Universe. However, CP violation in quarks is too small to support this explanation. So far, CP violation has not been observed in non-quark elementary particle systems. It has been shown that CP violation in leptons could generate the matter-antimatter disparity through a process called leptogenesis(4). Leptonic mixing, which appears in the standard model'  s charged current interactions(5,6), provides a potential source of CP violation through a complex phase dCP, which is required by some theoretical models of leptogenesis(7-9). This CP violation can be measured in muon neutrino to electron neutrino oscillations and the corresponding antineutrino oscillations, which are experimentally accessible using accelerator-produced beams as established by the Tokai-to-Kamioka (T2K) and NOvA experiments(10,11). Until now, the value of dCP has not been substantially constrained by neutrino oscillation experiments. Here we report a measurement using long-baseline neutrino and antineutrino oscillations observed by the T2K experiment that shows a large increase in the neutrino oscillation probability, excluding values of dCP that result in a large increase in the observed antineutrino oscillation probability at three standard deviations (3 sigma). The 3 sigma confidence interval for delta(CP), which is cyclic and repeats every 2p, is [-3.41, -0.03] for the so-called normal mass ordering and [-2.54, -0.32] for the inverted mass ordering. Our results indicate CP violation in leptons and our method enables sensitive searches for matter-antimatter asymmetry in neutrino oscillations using accelerator-produced neutrino beams. Future measurements with larger datasets will test whether leptonic CP violation is larger than the CP violation in quarks.


  
Germline Elongator mutations in Sonic Hedgehog medulloblastoma 期刊论文
NATURE, 2020, 580 (7803) : 396-+
作者:  Helmrich, S.;  Arias, A.;  Lochead, G.;  Wintermantel, T. M.;  Buchhold, M.;  Diehl, S.;  Whitlock, S.
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children(1,2), and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma(3). Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHH alpha subtype(4) and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U-34) position(5,6). Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems(7-9). Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.


  
Classification with a disordered dopantatom network in silicon 期刊论文
NATURE, 2020, 577 (7790) : 341-+
作者:  Vagnozzi, Ronald J.;  Maillet, Marjorie;  Sargent, Michelle A.;  Khalil, Hadi;  Johansen, Anne Katrine Z.;  Schwanekamp, Jennifer A.;  York, Allen J.;  Huang, Vincent;  Nahrendorf, Matthias;  Sadayappan, Sakthivel;  Molkentin, Jeffery D.
收藏  |  浏览/下载:24/0  |  提交时间:2020/07/03

Classification is an important task at which both biological and artificial neural networks excel(1,2). In machine learning, nonlinear projection into a high-dimensional feature space can make data linearly separable(3,4), simplifying the classification of complex features. Such nonlinear projections are computationally expensive in conventional computers. A promising approach is to exploit physical materials systems that perform this nonlinear projection intrinsically, because of their high computational density(5), inherent parallelism and energy efficiency(6,7). However, existing approaches either rely on the systems'  time dynamics, which requires sequential data processing and therefore hinders parallel computation(5,6,8), or employ large materials systems that are difficult to scale up(7). Here we use a parallel, nanoscale approach inspired by filters in the brain(1) and artificial neural networks(2) to perform nonlinear classification and feature extraction. We exploit the nonlinearity of hopping conduction(9-11) through an electrically tunable network of boron dopant atoms in silicon, reconfiguring the network through artificial evolution to realize different computational functions. We first solve the canonical two-input binary classification problem, realizing all Boolean logic gates(12) up to room temperature, demonstrating nonlinear classification with the nanomaterial system. We then evolve our dopant network to realize feature filters(2) that can perform four-input binary classification on the Modified National Institute of Standards and Technology handwritten digit database. Implementation of our material-based filters substantially improves the classification accuracy over that of a linear classifier directly applied to the original data(13). Our results establish a paradigm of silicon-based electronics for smallfootprint and energy-efficient computation(14).


  
Structural basis of energy transfer in Porphyridium purpureum phycobilisome 期刊论文
NATURE, 2020
作者:  Long, Haizhen;  Zhang, Liwei;  Lv, Mengjie;  Wen, Zengqi;  Zhang, Wenhao;  Chen, Xiulan;  Zhang, Peitao;  Li, Tongqing;  Chang, Luyuan;  Jin, Caiwei;  Wu, Guozhao;  Wang, Xi;  Yang, Fuquan;  Pei, Jianfeng;  Chen, Ping;  Margueron, Raphael;  Deng, Haiteng;  Zhu, Mingzhao;  Li, Guohong
收藏  |  浏览/下载:26/0  |  提交时间:2020/07/03

The cryo-electron microscopy structure of a phycobilisome from the red alga Porphyridium purpureum reveals how aromatic interactions between the linker proteins and the chromophores drive a unidirectional transfer of energy.


Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments(1). Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae(2-4), although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica(5) enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.