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Protein & Cell 2016年第7期7卷 533-537页

作者： Xu Jiang Shan Feng Yuling Chen Yun Feng haiteng deng MOE Key Laboratory of Bioinformatics School of Life SciencesTsinghua University Beijing 100084 China

Dear Editor, The mammalian target of rapamycin （mTOR）, as a critical energy sensor and cell-growth regulator, controls protein synthesis, autophagy and many important cellular processes through forming functional distinct complexes, mTORC1 and mTORC2, mTORC1 that is sensitive to rapamycin, regulates cell growth and protein synthesis, while mTORC2 that is insensitive to rapamycin, regulates cellular metabolism and the cytoskeletal organization （Gingras et al., 2001; Hay and Sonenberg, 2004）. Translation initiation is the rate-limiting step in protein synthesis, which proceeds through a multi- step process that can be divided into three major steps. First, eukaryotic translation initiation factor 2 （elF2） binds with GTP and methionyl-tRNA to form the ternary complex, which further binds to 40S ribosomal subunit with the help of elF1, elF1A, elF3 and elF5 resulting the preinitiation complex （PIC）. Second, the PIC binds to mRNA which is unwinded by the elF4F complex （including elF4E, elF4G, elF4A, elF4B）.

关键词： Phosphorylation Site Rapamycin Treatment Eukaryotic Translation Initiation Factor Mediate Phosphorylation Phosphorylation Peptide

p38α MAP kinase phosphorylates RCAN1 and regulates its interaction with calcineurin

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Science China(Life Sciences) 2012年第7期55卷 559-566页

作者： MA Lei TANG HaiPing REN Yan deng haiteng WU JiaWei WANG ZhiXin National Laboratory of Biomacromolecules Institute of Biophysics and Graduate University Chinese Academy of Sciences Beijing 100101 China School of Life Sciences Tsinghua University Beijing 100084 China Department of Biochemistry and Molecular Biology Beijing Normal University Beijing 100875 China

RCAN1, also known as DSCR1, is an endogenous regulator of calcineurin, a serine/threonine protein phosphatase that plays a critical role in many physiological processes. In this report, we demonstrate that p38a MAP kinase can phosphorylate RCAN1 at multiple sites in vitro and show that phospho-RCAN1 is a good protein substrate for calcineurin. In addition, we found that unphosphorylated RCANI noncompetitively inhibits calcineurin protein phosphatase activity and that the phosphorylation of RCAN1 by p38a MAP kinase decreases the binding affinity of RCAN1 for calcineurin. These findings reveal the molecular mechanism by which p38a MAP kinase regulates the function of RCAN1/calcineurin through phosphorylation.

关键词： p38a MAP kinase RCAN1 calcineurin phosphorylation

Large-scale identification of potential phase-separation proteins from plants using a cell-free system

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Molecular Plant 2023年第2期16卷 310-313页

作者： Honghong Zhang Fangyu Peng Chun He Yan Liu haiteng deng Xiaofeng Fang Center for Plant Biology School of Life SciencesTsinghua UniversityBejing 100084China MOE Key Laboratory of Bioinformatics School of Life SciencesTsinghua UniversityBeijing100084China

Dear Editor,Biomolecular condensates have emerged as key players in cellular processes and responses to stress(Alberti and Hyman,2021).Recent studies have revealed that most biomolecular condensates arise from liquid-liquid phase separation(Banani et al.,2017;Shin and Brangwynne,2017),a process that has been described in the field of polymer chemistry.

关键词： chemistry. separation phase

High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells

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Genomics, Proteomics & Bioinformatics 2022年第4期20卷 657-669页

作者： Songbiao Zhu Wenxi Ding Yuling Chen Weixuan Wang Renhua Xu Chongdong Liu Xiaohui Liu haiteng deng MOE Key Laboratory of Bioinformatics Center for Synthetic and Systematic BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine Guangdong Pharmaceutical UniversityGuangzhou 510006China School of Nursing Binzhou Medical UniversityYantai 264003China Department of Obstetrics and Gynecology Beijing Chao-Yang HospitalCapital Medical UniversityBeijing 100020China

Clear cell renal cell carcinoma(ccRCC)is a frequently occurring renal *** Von Hippel-Lindau disease tumor suppressor VHL,a known tumor suppressor gene,is frequently mutated in about 50%of patients with ***,it is unclear whether VHL influences the progression of ccRCC tumors expressing wild-type *** the present study,we found that higher expression of VHL was correlated with the better disease-free survival(DFS)in ccRCC patients using The Cancer Genome Atlas(TCGA)*** revealed that VHL overexpression in ccRCC cells inhibited epithelial-mesenchymal transition(EMT),sterol regulatory elementbinding protein 1(SREBP1)-regulated triglyceride synthesis,and cell *** analysis provided us a global view that VHL regulated four biological processes,including metabolism,immune regulation,apoptosis,and cell ***,we found that VHL overexpression led to up-regulated expression of proteins associated with antigen processing and interferonresponsive proteins,thus rendering ccRCC cells more sensitive to interferon *** defined an interferon-responsive signature(IRS)composed of ten interferon-responsive proteins,whose m RNA expression levels were positively correlated with DFS in ccRCC *** together,our results propose that the subset of ccRCC patients with high VHL expression benefit from immunotherapy.

关键词： Renal cancer VHL Immunogenicity Multi-omics Interferon

Bcl10 phosphorylation-dependent droplet-like condensation positively regulates DNA virus-induced innate immune signaling

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Science China(Life Sciences) 2023年第2期66卷 283-297页

作者： Dandan Yang Gaofeng Pei Shuangshuang Dong Wenhao Zhang haiteng deng Xueqiang Zhao Pilong Li Xin Lin Institute for Immunology School of MedicineTsinghua UniversityBeijing 100084China Beijing Advanced Innovation Center for Structural Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China MOE Key Laboratory of Bioinformatics School of Life SciencesTsinghua UniversityBeijing 100084China

B-cell lymphoma 10(Bcl10) is a scaffolding protein that functions as an upstream regulator of NF-κB signaling by forming a complex with Mucosa-associated lymphoid tissue lymphoma translocation protein 1(Malt1) and CARD-coiled coil protein family. This study showed that Bcl10 was involved in type I interferon(IFN) expression in response to DNA virus infection and that Bcl10-deficient mice were more susceptible to Herpes simplex virus 1(HSV-1) infection than control mice. Mechanistically,DNA virus infection can trigger Bcl10 recruitment to the STING-TBK1 complex, leading to Bcl10 phosphorylation by *** phosphorylated Bcl10 undergoes droplet-like condensation and forms oligomers, which induce TBK1 phosphorylation and translocation to the perinuclear region. The activated TBK1 phosphorylates IRF3, which induces the expression of type I *** study elucidates that Bcl10 induces an innate immune response by undergoing droplet-like condensation and participating in signalosome formation downstream of the c GAS-STING pathway.

关键词： Bcl10 DNA virus phosphorylation droplet condensation

Overexpression of SIRT3 disrupts mitochondrial proteostasis and cell cycle progression

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Protein & Cell 2016年第4期7卷 295-299页

作者： Xiaofei Wang Haiping Tang Yuling Chen Binghuan Chi Shiyu Wang Yang Lv Di WU Renshan Ge haiteng deng MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China Wenzhou Medical College Wenzhou 325035 China Center of Nephrology The General Hospital of the PLA Beijing 100853 China

Dear Editor, As a mitochondrial deacetylase, SIRT3 deacetylates many enzymes involved in central metabolism and maintains mitochondrial proteostasis （Verdin et al., 2010; Papa and Germain, 2014）. Substrates of SIRT3 include components of the respiratory complexes, proteins involved in fatty acid oxidation and TCA cycle （Yu et al., 2012）. SIRT3 activates MnSOD to maintain reactive oxygen species （ROS） home- ostasis and a loss of SIRT3 contributes to the age-associ- ated diseases （McDonnell et al., 2015; Qiu et al., 2010）. SIRT3 plays dual roles functioning as a tumor suppressor or a promoter in tumorigenesis and progression （Alhazzazi et al., 2011 ）. On one hand, SIRT3 regulates the cellular ROS level and maintains genomic stability, and mediates meta- bolic reprogramming to prevent tumorigenesis （Finley and Haigis, 2012）. As a result, the low expression of SIRT3 has been found in breast cancer, glioblastoma, colon cancer, osteosarcoma, prostate, and ovarian cancers （Kim et al., 2010; Finley and Haigis, 2012）. On the other hand, SIRT3 is a prosurvival factor that modulates p53 activities and is upregulated in oral cancer, the node-positive breast cancer, and bladder cancer （Ashraf et al., 2006; Alhazzazi et al., 2011）. These results suggest that SIRT3 possesses the tumor-type dependent function and its precise role needs to be elucidated in the context of a specific cancer. Clear cell renal cell carcinoma （ccRCC） is the most common histo- logical subtype of renal cancer （Cohen and McGovern, 2005）. The aims of the present study were to examine the expression of SIRT3 in ccRCC and to characterize effects of SIRT3 on tumorigenesis and progression using 293T human embryonic kidney cells as the model system that has cancer stem cell-like features （Debeb et al., 2010）.

关键词： Respiratory Complex 293T Human Embryonic Kidney SIRT3 Overexpression Cellular Reactive Oxygen Species Level 293T Human Embryonic Kidney Cell

Analysis of phosphorylation sites on autophagy proteins

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Protein & Cell 2015年第9期6卷 698-701页

作者： Wenzhi Feng Wenhao Zhang Hui Wang Lili Ma Di Miao Zexian Liu Yu Xue haiteng deng Li Yu PTN Program College of Life SciencePeking UniversityBeijing100871China Center for Biomedical Analysis Medical SchoolTsinghua UniversityBeijing100084China Key Laboratory of Cardiovascular Remodeling and Function Research Department of CardiologyQilu Hospital of Shandong UniversityJinan250012China Department of Biomedical Engineering College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China State Key Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University–Peking University Joint Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China

Autophagy is a lysosome-based degradation pathway,characterized by formation of a double-membrane vesicle named the *** autophagy,various cargos are engulfed and delivered to lysosomes(or the vacuole in yeast)for *** is an evolutionarily conserved pathway and plays important roles in various physiological and pathological conditions such as develop-ment,immunity,cancer and neuronal degeneration(Jiang and Mizushima,2014;Martin et al.,2014).

关键词：蛋白磷酸化自噬位点分析降解途径溶酶体双层膜液泡进化

Phosphorylation of Atg31 is required for autophagy

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Protein & Cell 2015年第4期6卷 288-296页

作者： Wenzhi Feng Tong Wu Xiaoyu Dan Yuling Chen Lin Li She Chen Di Miao haiteng deng Xinqi Gong Li Yu PTN Program College of Life Science Peking University Beijing 100871 China State Key Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University-Peking University Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China Center for Biomedical Analysis Tsinghua University Beijing 100084 China National Institute of Biological Sciences Beijing 102206 China Institute for Mathematical-Sciences Renmin-University of China Beijing 100872 China

Autophagy is an evolutionarily conserved cellular pro- cess which degrades intracellular contents. The Atg17- Atg31-Atg29 complex plays a key role in autophagy in- duction by various stimuli. In yeast, autophagy occurs with autophagosome formation at a special site near the vacuole named the pre-autophagosomal structure （PAS）. The Atg17-Atg31-Atg29 complex forms a scaffold for PAS organization, and recruits other autophagy-re- lated （Atg） proteins to the PAS. Here, we show that Atg31 is a phosphorylated protein. The phosphorylation sites on Atg31 were identified by mass spectrometry. Analy- sis of mutants in which the phosphorylated amino acids were replaced by alanine, either individually or in var- ious combinations, identified S174 as the functional phosphorylation site. An S174A mutant showed a simi- lar degree of autophagy impairment as an Atg31 deletion mutant. S174 phosphorylation is required for autophagy induced by various autophagy stimuli such as nitrogen starvation and rapamycin treatment. Mass spectrometry analysis showed that S174 is phosphorylated constitu- tively, and expression of a phosphorylation-mimic mu- tant （S174D） in the Atg31 deletion strain restores autophagy. In the S174A mutant, Atg9-positive vesicles accumulate at the PAS. Thus, S174 phosphorylation is required for formation of autophagosomes, possibly by facilitating the recycling of Atg9 from the PAS. Our data demonstrate the role of phosphorylation of Atg31 in autophagy.

关键词： autophagy Atg31 phosphorylation,autophagosome pre-autophagosomal structure (PAS)

The gain of hydrogen peroxide resistance benefits growth fitness in mycobacteria under stress

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Protein & Cell 2014年第3期5卷 182-185页

作者： Xiaojing Li Jun Tao Jiao Han Xinling Hu YulingChen haiteng deng Guangchun Zhang Xiaoxiang Hu Kaixia Mi CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology CAS Beijing 100101 China University of Chinese Academy of Sciences Beijing 100082 China School of Life Sciences Tsinghua University Beijing 100084 China School of Life Sciences China Agriculture University Beijing 100094 China Beijing Key Laboratory of Drug Resistance and Resistome Beijing 100101 China

Dear Editor, Tuberculosis （TB） is a formidable challenge to global health and is caused by an ancient pathogen, Mycobacteriurn tuberculosis （WHO, 2010）. In the pre-antibiotic era, TB killed 20% of adults in Europe and North America in the period from the seventeenth to the nineteenth centuries （Wilson, 2005）. Since antibiotics have been included in TB treatment regi- mens, millions of human lives have been saved by this che- motherapy. However, the standard anti-tuberculosis therapy is only effective for drug-susceptible TB but not for multi-drug resistant and extensively drug-resistant TB. Unfortunately, our knowledge of drug resistance in mycobacteria remains unclear and thus hampers the development of new anti- tubercular drugs. The basic mechanisms of drug resistance in mycobacteria are complicated and the outcome of drug resistance stems from evolution in the final analysis. Under- standing the evolutionary strategies used by M. tuberculosis might give new insights into designing control strategies against M. tuberculosis （Little et al,. 2012）.

关键词： Tuberculosis Reactive Oxygen Species Damage Growth Benefit Ferric Uptake Regulation Reactive Oxygen Species Stress

Capturing the hierarchically assorted modules of protein–protein interactions in the organized nucleome

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Molecular Plant 2023年第5期16卷 930-961页

作者： Shuaijian Dai Shichang Liu Chen Zhou Fengchao Yu Guang Zhu Wenhao Zhang haiteng deng Al Burlingame Weichuan Yu Tingliang Wang Ning Li Division of Life Science The Hong Kong University of Science and TechnologyHong Kong SARChina Department of Chemical and Biological Engineering The Hong Kong University of Science and TechnologyHong KongChina Tsinghua-Peking Joint Centre for Life Sciences Centre for Structural BiologySchoolof Life Sciences and Schoolof MedicineTsinghua UniversityBejing 100084China The Hk.UST Shenzhen-Hong Kong Collaborative Innovation Research Institute FutianShenzhenGuangdong 518057China Department of Electronic and Computer Engineering The Hong Kong University of Science and TechnologyHong Kong SARChina Department of Pharmaceutical Chemistry University of CaliforniaSan FranciscoSan FranciscoCAUSA

Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear *** decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions,we conducted two rounds of cross-linking mass spectrometry(XL-MS)analysis,one of which followed a quantitative double chemical cross-linking mass spectrometry(in vivo qXL-MS)workflow,and identified 24,140 unique crosslinks in total from the nuclei of soybean *** in vivo quantitative interactomics enabled the identification of 5340 crosslinks that can be converted into 1297 nuclear protein–protein interactions(PPIs),1220(94%)of which were non-confirmative(or novel)nuclear PPIs compared with those in *** were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex,*** analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules(NPIMs)that contain the condensate-forming protein(s)and the intrinsically disordered region–containing proteins,*** NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the ***,these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph,including genome and nucleolus *** combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear *** pipeline was able to capture both nuclear protein complexes and nuclear bodies,construct the topological architectures of PPI modules and module variants in the nucleome,and probably map the protein compositions of biomolecular condensates.

关键词： nucleome 4C interactomics in vivo qXL-MS biomolecular modulomics CHAMPION 4D biomolecular modulomes