贺新义

研究员

研究方向

硫修饰DNA识别蛋白

硫修饰DNA及其识别蛋白的复合物结构,发现硫原子被巧妙包埋于其中一个保守结构域(Sulfur Binding Domain, SBD)的浅表疏水坑中。与氧原子相比,硫原子具有更大的原子半径,导致其对外层电子的吸引作用明显减弱,呈现出较弱的电负性,赋予硫原子疏水的特性。SBD正好利用这个细微差异来区分硫修饰DNA和普通DNA

代表论著

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    Xiankun Wang, Yuchun Zhao, Yaojie Gao, Xiangkun Luo, Aiqing Du, Zixin Deng, Zabriskie TM, Xinyi He*, Ming Jiang*. A [3Fe-4S] cluster and tRNA-dependent aminoacyltransferase BlsK in the biosynthesis of Blasticidin S. Proc Natl Acad Sci  U S A. 2021 Jul 27;118(30):e2102318118. doi: 10.1073/pnas.2102318118.

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    Hao Yu, Jiayi Li, Guang Liu, Gong Zhao, Yuli Wang, Wenyue Hu, Zixin Deng, Geng Wu, Jianhua Gan, Yi-Lei Zhao*, Xinyi He*. DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses.  Nucleic Acids Research 2020 Sep 4;48(15):8755-8766. doi: 10.1093/nar/gkaa574.

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    Hongliang Qian, Hao Yu, Peifei Li, E Zhu, Qingqing Yao, Cui Tai, Zixin Deng, Kenn Gerdes, Xinyi He*, Jianhua Gan*, Hong-Yu Ou*. Toxin-antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA-KacT complex. Nucleic Acids Research. 2019 Aug 22;47(14):7690-7702.

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    Guang Liu, Wencheng Fu, Zhengyi Zhang, Yao He, Hao Yu, Yuli Wang, Xiaolei Wang, Yi-Lei Zhao, Zixin Deng, Geng Wu*, Xinyi He*. Structural basis for the recognition of sulfur in phosphorothioated DNA. Nature Communications. 2018 Nov 8;9(1):4689.

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    Hao Yu, Guang Liu, Gong Zhao, Wenyue Hu, Geng Wu, Zixin Deng, Xinyi He*. Identification of a conserved DNA sulfur recognition domain by characterizing the phosphorothioate-specific endonuclease SprMcrA from Streptomyces pristinaespiralis. Molecular Microbiology. 2018 Nov;110(3):484-497.

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    Xiankun Wang, Aiqing Du, Guiyang Yu, Zixin Deng, Xinyi He*. Guanidine N-methylation by BlsL Is Dependent on Acylation of Beta-amine Arginine in the Biosynthesis of Blasticidin S. Front Microbiol. 2017 Aug 22;8:1565.

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    Gong Zhao, Geng Wu, Yan Zhang, Guang Liu, Tiesheng Han, Zixin Deng, and Xinyi He*. Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry. Nucleic Acids Research 2014, 42(12): 8115-8124.

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    Tiesheng Han, Megumu Yamada-Mabuchi, Gong Zhao, Li Li, Guang Liu, Hong-Yu Ou, Zixin Deng, Yu Zheng*, and Xinyi He*. Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins. Nucleic Acids Research 2015, 43(2): 1147-1159.

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    Jun Feng, Jun Wu, Jie Gao, Zhigui Xia, Zixin Deng, and Xinyi He*. Biosynthesis of the methylarginine residue of peptidyl nucleoside arginomycin in Streptomyces arginensis NRRL 15941. Applied and Environmental Microbiology 2014, 80(16): 5021-5027.

获奖情况

  • 上海交通大学晨星青年学者奖励计划SMC优秀青年教师 (A类)
  • 获得2015年教育部自然科学一等奖(排名第四)
  • 2005年中国高校十大科技进展(第二作者)
  • 国家自然科学基金面上项目 杀稻瘟菌素类肽核苷关键生物合成步骤和新颖抗性机制的酶学研究 (2015.01-2018.12) 85万 主持
  • 国家自然科学基金面上项目 天蓝色链霉菌中甲基化修饰依赖型限制系统的发现和表征 (2012.01-2015.12) 60万 主持
  • 国家自然科学基金面上项目 天蓝色链霉菌中一种DNA硫化修饰依赖型限制系统的发现和功能研究 (2010.01-2012.12) 35万 主持
  • 国家自然科学基金面上项目 DNA修饰依赖型HNH核酸内切酶切割活性机制及应用研究 (2019.01-2022.12) 60万 主持
  • 国家自然科学基金面上项目 硫修饰DNA结合蛋白的发现及其结构和功能研究 (2012.01-2014.12) 63万 主持
  • 科技部973子课题 FR-008基因组最小化(2012.01-2016.12)80万 主持

承担项目