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Action of a minimal contractile bactericidal nanomachine 期刊论文
NATURE, 2020, 580 (7805) : 658-+
作者:  Peng, Ruchao;  Xu, Xin;  Jing, Jiamei;  Wang, Min;  Peng, Qi;  Liu, Sheng;  Wu, Ying;  Bao, Xichen;  Wang, Peiyi;  Qi, Jianxun;  Gao, George F.;  Shi, Yi
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

The authors report near-atomic resolution structures of the R-type bacteriocin from Pseudomonas aeruginosa in the pre-contraction and post-contraction states, and these structures provide insight into the mechanism of action of molecular syringes.


R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics(1-4). Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold(1,2). Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage(5). Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes  the dissociation then initiates a cascade of events leading to sheath contraction  and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.


  
Recycling and metabolic flexibility dictate life in the lower oceanic crust 期刊论文
NATURE, 2020, 579 (7798) : 250-+
作者:  Zhou, Peng;  Yang, Xing-Lou;  Wang, Xian-Guang;  Hu, Ben;  Zhang, Lei;  Zhang, Wei;  Si, Hao-Rui;  Zhu, Yan;  Li, Bei;  Huang, Chao-Lin;  Chen, Hui-Dong;  Chen, Jing;  Luo, Yun;  Guo, Hua;  Jiang, Ren-Di;  Liu, Mei-Qin;  Chen, Ying;  Shen, Xu-Rui;  Wang, Xi;  Zheng, Xiao-Shuang;  Zhao, Kai;  Chen, Quan-Jiao;  Deng, Fei;  Liu, Lin-Lin;  Yan, Bing;  Zhan, Fa-Xian;  Wang, Yan-Yi;  Xiao, Geng-Fu;  Shi, Zheng-Li
收藏  |  浏览/下载:37/0  |  提交时间:2020/05/13

The lithified lower oceanic crust is one of Earth'  s last biological frontiers as it is difficult to access. It is challenging for microbiota that live in marine subsurface sediments or igneous basement to obtain sufficient carbon resources and energy to support growth(1-3) or to meet basal power requirements(4) during periods of resource scarcity. Here we show how limited and unpredictable sources of carbon and energy dictate survival strategies used by low-biomass microbial communities that live 10-750 m below the seafloor at Atlantis Bank, Indian Ocean, where Earth'  s lower crust is exposed at the seafloor. Assays of enzyme activities, lipid biomarkers, marker genes and microscopy indicate heterogeneously distributed and viable biomass with ultralow cell densities (fewer than 2,000 cells per cm(3)). Expression of genes involved in unexpected heterotrophic processes includes those with a role in the degradation of polyaromatic hydrocarbons, use of polyhydroxyalkanoates as carbon-storage molecules and recycling of amino acids to produce compounds that can participate in redox reactions and energy production. Our study provides insights into how microorganisms in the plutonic crust are able to survive within fractures or porous substrates by coupling sources of energy to organic and inorganic carbon resources that are probably delivered through the circulation of subseafloor fluids or seawater.


  
Improved protein structure prediction using potentials from deep learning 期刊论文
NATURE, 2020, 577 (7792) : 706-+
作者:  Ma, Runze;  Cao, Duanyun;  Zhu, Chongqin;  Tian, Ye;  Peng, Jinbo;  Guo, Jing;  Chen, Ji;  Li, Xin-Zheng;  Francisco, Joseph S.;  Zeng, Xiao Cheng;  Xu, Li-Mei;  Wang, En-Ge;  Jiang, Ying
收藏  |  浏览/下载:143/0  |  提交时间:2020/07/03

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence(1). This problem is of fundamental importance as the structure of a protein largely determines its function(2)  however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures(3). Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force(4) that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction(5) (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores(6) of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined(7).


  
Assessing progress towards sustainable development over space and time 期刊论文
NATURE, 2020, 577 (7788) : 74-+
作者:  Xu, Zhenci;  Chau, Sophia N.;  Chen, Xiuzhi;  Zhang, Jian;  Li, Yingjie;  Dietz, Thomas;  Wang, Jinyan;  Winkler, Julie A.;  Fan, Fan;  Huang, Baorong;  Li, Shuxin;  Wu, Shaohua;  Herzberger, Anna;  Tang, Ying;  Hong, Dequ;  Li, Yunkai;  Liu, Jianguo
收藏  |  浏览/下载:10/0  |  提交时间:2020/05/13

To address global challenges(1-4), 193 countries have committed to the 17 United Nations Sustainable Development Goals (SDGs)(5). Quantifying progress towards achieving the SDGs is essential to track global efforts towards sustainable development and guide policy development and implementation. However, systematic methods for assessing spatio-temporal progress towards achieving the SDGs are lacking. Here we develop and test systematic methods to quantify progress towards the 17 SDGs at national and subnational levels in China. Our analyses indicate that China'  s SDG Index score (an aggregate score representing the overall performance towards achieving all 17 SDGs) increased at the national level from 2000 to 2015. Every province also increased its SDG Index score over this period. There were large spatio-temporal variations across regions. For example, eastern China had a higher SDG Index score than western China in the 2000s, and southern China had a higher SDG Index score than northern China in 2015. At the national level, the scores of 13 of the 17 SDGs improved over time, but the scores of four SDGs declined. This study suggests the need to track the spatio-temporal dynamics of progress towards SDGs at the global level and in other nations.


  
Palmitoylation of NOD1 and NOD2 is required for bacterial sensing 期刊论文
SCIENCE, 2019, 366 (6464) : 460-+
作者:  Lu, Yan;  Zheng, Yuping;  Coyaud, Etienne;  Zhang, Chao;  Selvabaskaran, Apiraam;  Yu, Yuyun;  Xu, Zizhen;  Weng, Xialian;  Chen, Ji Shun;  Meng, Ying;  Warner, Neil;  Cheng, Xiawei;  Liu, Yangyang;  Yao, Bingpeng;  Hu, Hu;  Xia, Zonping;  Muise, Aleixo M.;  Klip, Amira;  Brumell, John H.;  Girardin, Stephen E.;  Ying, Songmin;  Fairn, Gregory D.;  Raught, Brian;  Sun, Qiming;  Neculai, Dante
收藏  |  浏览/下载:13/0  |  提交时间:2019/11/27
HNRNPK maintains epidermal progenitor function through transcription of proliferation genes and degrading differentiation promoting mRNAs 期刊论文
NATURE COMMUNICATIONS, 2019, 10
作者:  Li, Jingting;  Chen, Yifang;  Xu, Xiaojun;  Jones, Jackson;  Tiwari, Manisha;  Ling, Ji;  Wang, Ying;  Harismendy, Olivier;  Sen, George L.
收藏  |  浏览/下载:9/0  |  提交时间:2019/11/27
Tip60-mediated lipin 1 acetylation and ER translocation determine triacylglycerol synthesis rate 期刊论文
NATURE COMMUNICATIONS, 2018, 9
作者:  Li, Terytty Yang;  Song, Lintao;  Sun, Yu;  Li, Jingyi;  Yi, Cong;  Lam, Sin Man;  Xu, Dijin;  Zhou, Linkang;  Li, Xiaotong;  Yang, Ying;  Zhang, Chen-Song;  Xie, Changchuan;  Huang, Xi;  Shui, Guanghou;  Lin, Shu-Yong;  Reue, Karen;  Lin, Sheng-Cai
收藏  |  浏览/下载:10/0  |  提交时间:2019/11/27
Resetting histone modifications during human parental-to-zygotic transition 期刊论文
SCIENCE, 2019, 365 (6451) : 353-+
作者:  Xia, Weikun;  Xu, Jiawei;  Yu, Guang;  Yao, Guidong;  Xu, Kai;  Ma, Xueshan;  Zhang, Nan;  Liu, Bofeng;  Li, Tong;  Lin, Zili;  Chen, Xia;  Li, Lijia;  Wang, Qiujun;  Shi, Dayuan;  Shi, Senlin;  Zhang, Yile;  Song, Wenyan;  Jin, Haixia;  Hu, Linli;  Bu, Zhiqin;  Wang, Yang;  Na, Jie;  Xie, Wei;  Sun, Ying-Pu
收藏  |  浏览/下载:11/0  |  提交时间:2019/11/27
Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process 期刊论文
NATURE COMMUNICATIONS, 2019, 10
作者:  Zhao, Zheng;  Zheng, Xiaoyan;  Du, Lili;  Xiong, Yu;  He, Wei;  Gao, Xiuxiu;  Li, Chunli;  Liu, Yingjie;  Xu, Bin;  Zhang, Jing;  Song, Fengyan;  Yu, Ying;  Zhao, Xueqian;  Cai, Yuanjing;  He, Xuewen;  Kwok, Ryan T. K.;  Lam, Jacky W. Y.;  Huang, Xuhui;  Phillips, David Lee;  Wang, Hua;  Tang, Ben Zhong
收藏  |  浏览/下载:13/0  |  提交时间:2019/11/27
Loss-of-function mutations in QRICH2 cause male infertility with multiple morphological abnormalities of the sperm flagella 期刊论文
NATURE COMMUNICATIONS, 2019, 10
作者:  Shen, Ying;  Zhang, Feng;  Li, Fuping;  Jiang, Xiaohui;  Yang, Yihong;  Li, Xiaoliang;  Li, Weiyu;  Wang, Xiang;  Cheng, Juan;  Liu, Mohan;  Zhang, Xueguang;  Yuan, Guiping;  Pei, Xue;  Cai, Kailai;  Hu, Fengyun;  Sun, Jianfeng;  Yan, Lanzhen;  Tang, Li;  Jiang, Chuan;  Tu, Wenling;  Xu, Jinyan;  Wu, Haojuan;  Kong, Weiqi;  Li, Shuying;  Wang, Ke;  Sheng, Kai;  Zhao, Xudong;  Yue, Huanxun;  Yang, Xiaoyu;  Xu, Wenming
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/27