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Insights into the assembly and activation of the microtubule nucleator gamma-TuRC 期刊论文
NATURE, 2020, 578 (7795) : 467-+
作者:  Cyranoski, David
收藏  |  浏览/下载:36/0  |  提交时间:2020/07/03

Microtubules are dynamic polymers of alpha- and beta-tubulin and have crucial roles in cell signalling, cell migration, intracellular transport and chromosome segregation(1). They assemble de novo from alpha beta-tubulin dimers in an essential process termed microtubule nucleation. Complexes that contain the protein gamma-tubulin serve as structural templates for the microtubule nucleation reaction(2). In vertebrates, microtubules are nucleated by the 2.2-megadalton gamma-tubulin ring complex (gamma-TuRC), which comprises gamma-tubulin, five related gamma-tubulin complex proteins (GCP2-GCP6) and additional factors(3). GCP6 is unique among the GCP proteins because it carries an extended insertion domain of unknown function. Our understanding of microtubule formation in cells and tissues is limited by a lack of high-resolution structural information on the gamma-TuRC. Here we present the cryo-electron microscopy structure of gamma-TuRC from Xenopus laevis at 4.8 angstrom global resolution, and identify a 14-spoked arrangement of GCP proteins and gamma-tubulins in a partially flexible open left-handed spiral with a uniform sequence of GCP variants. By forming specific interactions with other GCP proteins, the GCP6-specific insertion domain acts as a scaffold for the assembly of the gamma-TuRC. Unexpectedly, we identify actin as a bona fide structural component of the gamma-TuRC with functional relevance in microtubule nucleation. The spiral geometry of gamma-TuRC is suboptimal for microtubule nucleation and a controlled conformational rearrangement of the gamma-TuRC is required for its activation. Collectively, our cryo-electron microscopy reconstructions provide detailed insights into the molecular organization, assembly and activation mechanism of vertebrate gamma-TuRC, and will serve as a framework for the mechanistic understanding of fundamental biological processes associated with microtubule nucleation, such as meiotic and mitotic spindle formation and centriole biogenesis(4).


The cryo-EM structure of the gamma-tubulin ring complex (gamma-TuRC) from Xenopus laevis provides insights into the molecular organization of the complex, and shows that actin is a structural component that is functionally relevant to microtubule nucleation.


  
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:17/0  |  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.


  
Mechanisms and therapeutic implications of hypermutation in gliomas 期刊论文
NATURE, 2020, 580 (7804) : 517-+
作者:  Feng, Kaibo;  Quevedo, Raundi E.;  Kohrt, Jeffrey T.;  Oderinde, Martins S.;  Reilly, Usa;  White, M. Christina
收藏  |  浏览/下载:43/0  |  提交时间:2020/07/03

A high tumour mutational burden (hypermutation) is observed in some gliomas(1-5)  however, the mechanisms by which hypermutation develops and whether it predicts the response to immunotherapy are poorly understood. Here we comprehensively analyse the molecular determinants of mutational burden and signatures in 10,294 gliomas. We delineate two main pathways to hypermutation: a de novo pathway associated with constitutional defects in DNA polymerase and mismatch repair (MMR) genes, and a more common post-treatment pathway, associated with acquired resistance driven by MMR defects in chemotherapy-sensitive gliomas that recur after treatment with the chemotherapy drug temozolomide. Experimentally, the mutational signature of post-treatment hypermutated gliomas was recapitulated by temozolomide-induced damage in cells with MMR deficiency. MMR-deficient gliomas were characterized by a lack of prominent T cell infiltrates, extensive intratumoral heterogeneity, poor patient survival and a low rate of response to PD-1 blockade. Moreover, although bulk analyses did not detect microsatellite instability in MMR-deficient gliomas, single-cell whole-genome sequencing analysis of post-treatment hypermutated glioma cells identified microsatellite mutations. These results show that chemotherapy can drive the acquisition of hypermutated populations without promoting a response to PD-1 blockade and supports the diagnostic use of mutational burden and signatures in cancer.


Temozolomide therapy seems to lead to mismatch repair deficiency and hypermutation in gliomas, but not to an increase in response to immunotherapy.


  
Parental-to-embryo switch of chromosome organization in early embryogenesis 期刊论文
NATURE, 2020: 142-+
作者:  Kim, Eugene;  Kerssemakers, Jacob;  Shaltiel, Indra A.;  Haering, Christian H.;  Dekker, Cees
收藏  |  浏览/下载:26/0  |  提交时间:2020/07/03

Single-cell allelic HiC analysis, combined with allelic gene expression and chromatin states, reveals parent-of-origin-specific dynamics of chromosome organization and gene expression during mouse preimplantation development.


Paternal and maternal epigenomes undergo marked changes after fertilization(1). Recent epigenomic studies have revealed the unusual chromatin landscapes that are present in oocytes, sperm and early preimplantation embryos, including atypical patterns of histone modifications(2-4) and differences in chromosome organization and accessibility, both in gametes(5-8) and after fertilization(5,8-10). However, these studies have led to very different conclusions: the global absence of local topological-associated domains (TADs) in gametes and their appearance in the embryo(8,9) versus the pre-existence of TADs and loops in the zygote(5,11). The questions of whether parental structures can be inherited in the newly formed embryo and how these structures might relate to allele-specific gene regulation remain open. Here we map genomic interactions for each parental genome (including the X chromosome), using an optimized single-cell high-throughput chromosome conformation capture (HiC) protocol(12,13), during preimplantation in the mouse. We integrate chromosome organization with allelic expression states and chromatin marks, and reveal that higher-order chromatin structure after fertilization coincides with an allele-specific enrichment of methylation of histone H3 at lysine 27. These early parental-specific domains correlate with gene repression and participate in parentally biased gene expression-including in recently described, transiently imprinted loci(14). We also find TADs that arise in a non-parental-specific manner during a second wave of genome assembly. These de novo domains are associated with active chromatin. Finally, we obtain insights into the relationship between TADs and gene expression by investigating structural changes to the paternal X chromosome before and during X chromosome inactivation in preimplantation female embryos(15). We find that TADs are lost as genes become silenced on the paternal X chromosome but linger in regions that escape X chromosome inactivation. These findings demonstrate the complex dynamics of three-dimensional genome organization and gene expression during early development.


  
An engineered PET depolymerase to break down and recycle plastic bottles 期刊论文
NATURE, 2020, 580 (7802) : 216-+
作者:  Zhao, Evan Wenbo;  Liu, Tao;  Jonsson, Erlendur;  Lee, Jeongjae;  Temprano, Israel;  Jethwa, Rajesh B.;  Wang, Anqi;  Smith, Holly;  Carretero-Gonzalez, Javier;  Song, Qilei;  Grey, Clare P.
收藏  |  浏览/下载:103/0  |  提交时间:2020/07/03

Present estimates suggest that of the 359 million tons of plastics produced annually worldwide(1), 150-200 million tons accumulate in landfill or in the natural environment(2). Poly(ethylene terephthalate) (PET) is the most abundant polyester plastic, with almost 70 million tons manufactured annually worldwide for use in textiles and packaging(3). The main recycling process for PET, via thermomechanical means, results in a loss of mechanical properties(4). Consequently, de novo synthesis is preferred and PET waste continues to accumulate. With a high ratio of aromatic terephthalate units-which reduce chain mobility-PET is a polyester that is extremely difficult to hydrolyse(5). Several PET hydrolase enzymes have been reported, but show limited productivity(6,7). Here we describe an improved PET hydrolase that ultimately achieves, over 10 hours, a minimum of 90 per cent PET depolymerization into monomers, with a productivity of 16.7 grams of terephthalate per litre per hour (200 grams per kilogram of PET suspension, with an enzyme concentration of 3 milligrams per gram of PET). This highly efficient, optimized enzyme outperforms all PET hydrolases reported so far, including an enzyme(8,9) from the bacterium Ideonella sakaiensis strain 201-F6 (even assisted by a secondary enzyme(10)) and related improved variants(11-14) that have attracted recent interest. We also show that biologically recycled PET exhibiting the same properties as petrochemical PET can be produced from enzymatically depolymerized PET waste, before being processed into bottles, thereby contributing towards the concept of a circular PET economy.


Computer-aided engineering produces improvements to an enzyme that breaks down poly(ethylene terephthalate) (PET) into its constituent monomers, which are used to synthesize PET of near-petrochemical grade that can be further processed into bottles.


  
Hidden linkages between resources and economy: A "Beyond-GDP" approach using alternative welfare indicators 期刊论文
ECOLOGICAL ECONOMICS, 2020, 169
作者:  Kalimeris, Panos;  Bithas, Kostas;  Richardson, Clive;  Nijkamp, Peter
收藏  |  浏览/下载:34/0  |  提交时间:2020/07/02
Beyond GDP  Material flow analysis (MFA)  Dematerialization  Material intensity (MI)  Decoupling  ISEW  HDI  GPI  (de)growth  Sustainability  Welfare measurement  
Early Holocene crop cultivation and landscape modification in Amazonia 期刊论文
NATURE, 2020, 581 (7807) : 190-+
作者:  Hendershot, J. Nicholas;  Smith, Jeffrey R.;  Anderson, Christopher B.;  Letten, Andrew D.;  Frishkoff, Luke O.;  Zook, Jim R.;  Fukami, Tadashi;  Daily, Gretchen C.
收藏  |  浏览/下载:41/0  |  提交时间:2020/07/03

The onset of plant cultivation is one of the most important cultural transitions in human history(1-4). Southwestern Amazonia has previously been proposed as an early centre of plant domestication, on the basis of molecular markers that show genetic similarities between domesticated plants and wild relatives(4-6). However, the nature of the early human occupation of southwestern Amazonia, and the history of plant cultivation in this region, are poorly understood. Here we document the cultivation of squash (Cucurbita sp.) at about 10,250 calibrated years before present (cal. yr bp), manioc (Manihot sp.) at about 10,350 cal. yr bp and maize (Zea mays) at about 6,850 cal. yr bp, in the Llanos de Moxos (Bolivia). We show that, starting at around 10,850 cal. yr bp, inhabitants of this region began to create a landscape that ultimately comprised approximately 4,700 artificial forest islands within a treeless, seasonally flooded savannah. Our results confirm that the Llanos de Moxos is a hotspot for early plant cultivation and demonstrate that-ever since their arrival in Amazonia-humans have markedly altered the landscape, with lasting repercussions for habitat heterogeneity and species conservation.


  
Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate 期刊论文
NATURE, 2020, 579 (7800) : 586-+
作者:  Ng, Andrew H.;  Nguyen, Taylor H.;  Gomez-Schiavon, Mariana;  Dods, Galen;  Langan, Robert A.;  Boyken, Scott E.;  Samson, Jennifer A.;  Waldburger, Lucas M.;  Dueber, John E.;  Baker, David;  El-Samad, Hana
收藏  |  浏览/下载:43/0  |  提交时间:2020/07/03

A genetic mouse model is used to reveal a two-pronged mechanism of fructose-induced de novo lipogenesis in the liver, in which fructose catabolism in hepatocytes provides a signal to promote lipogenesis, whereas fructose metabolism by the gut microbiota provides acetate as a substrate to feed lipogenesis.


Consumption of fructose has risen markedly in recent decades owing to the use of sucrose and high-fructose corn syrup in beverages and processed foods(1), and this has contributed to increasing rates of obesity and non-alcoholic fatty liver disease(2-4). Fructose intake triggers de novo lipogenesis in the liver(4-6), in which carbon precursors of acetyl-CoA are converted into fatty acids. The ATP citrate lyase (ACLY) enzyme cleaves cytosolic citrate to generate acetyl-CoA, and is upregulated after consumption of carbohydrates(7). Clinical trials are currently pursuing the inhibition of ACLY as a treatment for metabolic diseases(8). However, the route from dietary fructose to hepatic acetyl-CoA and lipids remains unknown. Here, using in vivo isotope tracing, we show that liver-specific deletion of Acly in mice is unable to suppress fructose-induced lipogenesis. Dietary fructose is converted to acetate by the gut microbiota(9), and this supplies lipogenic acetyl-CoA independently of ACLY(10). Depletion of the microbiota or silencing of hepatic ACSS2, which generates acetyl-CoA from acetate, potently suppresses the conversion of bolus fructose into hepatic acetyl-CoA and fatty acids. When fructose is consumed more gradually to facilitate its absorption in the small intestine, both citrate cleavage in hepatocytes and microorganism-derived acetate contribute to lipogenesis. By contrast, the lipogenic transcriptional program is activated in response to fructose in a manner that is independent of acetyl-CoA metabolism. These data reveal a two-pronged mechanism that regulates hepatic lipogenesis, in which fructolysis within hepatocytes provides a signal to promote the expression of lipogenic genes, and the generation of microbial acetate feeds lipogenic pools of acetyl-CoA.


  
FERONIA controls pectin- and nitric oxide-mediated male-female interaction 期刊论文
NATURE, 2020, 579 (7800) : 561-+
作者:  Venkadesan, Madhusudhan;  Yawar, Ali;  Eng, Carolyn M.;  Dias, Marcelo A.;  Singh, Dhiraj K.;  Tommasini, Steven M.;  Haims, Andrew H.;  Bandi, Mahesh M.;  Mandre, Shreyas
收藏  |  浏览/下载:41/0  |  提交时间:2020/07/03

Species that propagate by sexual reproduction actively guard against the fertilization of an egg by multiple sperm (polyspermy). Flowering plants rely on pollen tubes to transport their immotile sperm to fertilize the female gametophytes inside ovules. In Arabidopsis, pollen tubes are guided by cysteine-rich chemoattractants to target the female gametophyte(1,2). The FERONIA receptor kinase has a dual role in ensuring sperm delivery and blocking polyspermy(3). It has previously been reported that FERONIA generates a female gametophyte environment that is required for sperm release(4). Here we show that FERONIA controls several functionally linked conditions to prevent the penetration of female gametophytes by multiple pollen tubes in Arabidopsis. We demonstrate that FERONIA is crucial for maintaining de-esterified pectin at the filiform apparatus, a region of the cell wall at the entrance to the female gametophyte. Pollen tube arrival at the ovule triggers the accumulation of nitric oxide at the filiform apparatus in a process that is dependent on FERONIA and mediated by de-esterified pectin. Nitric oxide nitrosates both precursor and mature forms of the chemoattractant LURE1(1), respectively blocking its secretion and interaction with its receptor, to suppress pollen tube attraction. Our results elucidate a mechanism controlled by FERONIA in which the arrival of the first pollen tube alters ovular conditions to disengage pollen tube attraction and prevent the approach and penetration of the female gametophyte by late-arriving pollen tubes, thus averting polyspermy.


FERONIA prevents polyspermy in Arabidopsis by enabling pectin-stimulated nitric oxide accumulation at the filiform apparatus after the first pollen tube arrives, which disengages LURE1 chemoattraction to prevent late-arriving pollen tubes from entering the ovule.


  
A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds 期刊论文
NATURE, 2020, 580 (7803) : 409-+
作者:  Al-Shayeb, Basem;  Sachdeva, Rohan;  Chen, Lin-Xing;  Ward, Fred;  Munk, Patrick;  Devoto, Audra;  Castelle, Cindy J.;  Olm, Matthew R.;  Bouma-Gregson, Keith;  Amano, Yuki;  He, Christine;  Meheust, Raphael;  Brooks, Brandon;  Thomas, Alex;  Levy, Adi;  Matheus-Carnevali, Paula;  Sun, Christine;  Goltsman, Daniela S. A.;  Borton, Mikayla A.;  Sharrar, Allison;  Jaffe, Alexander L.;  Nelson, Tara C.;  Kantor, Rose;  Keren, Ray;  Lane, Katherine R.;  Farag, Ibrahim F.;  Lei, Shufei;  Finstad, Kari;  Amundson, Ronald;  Anantharaman, Karthik;  Zhou, Jinglie;  Probst, Alexander J.;  Power, Mary E.;  Tringe, Susannah G.;  Li, Wen-Jun;  Wrighton, Kelly;  Harrison, Sue;  Morowitz, Michael;  Relman, David A.;  Doudna, Jennifer A.;  Lehours, Anne-Catherine;  Warren, Lesley;  Cate, Jamie H. D.;  Santini, Joanne M.;  Banfield, Jillian F.
收藏  |  浏览/下载:67/0  |  提交时间:2020/07/03

Mycobacterium tuberculosis (Mtb) is an obligate human pathogen and the causative agent of tuberculosis(1-3). Although Mtb can synthesize vitamin B-12 (cobalamin) de novo, uptake of cobalamin has been linked to pathogenesis of tuberculosis2. Mtb does not encode any characterized cobalamin transporter(4-6)  however, the gene rv1819c was found to be essential for uptake of cobalamin(1). This result is difficult to reconcile with the original annotation of Rv1819c as a protein implicated in the transport of antimicrobial peptides such as bleomycin(7). In addition, uptake of cobalamin seems inconsistent with the amino acid sequence, which suggests that Rv1819c has a bacterial ATP-binding cassette (ABC)-exporter fold1. Here, we present structures of Rv1819c, which reveal that the protein indeed contains the ABC-exporter fold, as well as a large water-filled cavity of about 7,700 angstrom(3), which enables the protein to transport the unrelated hydrophilic compounds bleomycin and cobalamin. On the basis of these structures, we propose that Rv1819c is a multi-solute transporter for hydrophilic molecules, analogous to the multidrug exporters of the ABC transporter family, which pump out structurally diverse hydrophobic compounds from cells(8-11).