贺新义
  研究员
  链霉菌异常修饰-限制系统

  Email: xyhe@sjtu.edu.cn 

 

 

       贺新义:男,1975 年11 月出生,博士,上海交通大学微生物学研究员,国家自然科学基金委创新研究群体科学基金项目研究骨干。研究兴趣一直聚焦于核苷酸代谢,包括基础代谢中DNA磷硫酰化,羟甲基化,糖羟甲基化等异常修饰形成和识别的分子机理;以及次级代谢中具有良好生物活性的核苷类抗生素的生物合成,如杀稻瘟菌素,米多霉素和精霉素的生物合成的酶学研究。近五年来已发表第一或通讯作者SCI论文14篇,合作论文发表在《自然》杂志上并被评为2011年度中国科学十大进展;获得授权发明专利3项;先后主持4项国家自然科学基金项目;2004、05、09、10和14年度上海交通大学教师年终考核优秀;2010年获得上海交通大学SMC-晨星青年学者奖励计划 A类;相关研究成果获得“2005年中国高校十大科技进展”。并担任Journal of Biochemistry and Molecular Biology Research (ISSN2313-7177) 编委。
 

教育经历:

       2012/08-2013/08,访问学者,美国新英格兰生物实验室

       2004/03-2008/06,上海交通大学,生命科学技术学院,博士

       1998/09-2001/06,华中农业大学,生命科学技术学院,硕士

       1994/09-1998/06,华中农业大学,生命科学技术学院,学士

 

工作经历:

       2015/01-        上海交通大学微生物代谢国家重点实验室,研究员

       2014/01-2014/12    上海交通大学微生物代谢国家重点实验室,副研究员

       2010/01-2013/12    上海交通大学微生物代谢国家重点实验室,副教授

       2003/09-2009/12    上海交通大学,生命科学技术学院生物工程系,讲师

       2001/09-2003/08    上海交通大学,生命科学技术学院生物工程系,助教

 

研究方向:

       1)细菌核苷酸修饰及识别的酶学研究;

       2)核苷类抗生素的生物合成。

 

Figure 1. Structures of MilB by itself and its catalytically inactive E103A. (Zhao, et al. Nucleic Acids Research, 2014)

 

 

Figure 2  The proposed biosynthesis pathway of MIL. (Wu, et al. Chembiochem, 2012)

Figure 3  Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA (Liu, et al. PLoS Genet. 2010 )

 

代表论文:( * 为通讯作者)

1.    Xiufen Zhou, Xinyi He#, Aiying Li, Fang Lei, Tobias Kieser, and Zixin Deng. Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66. Applied and Environmental Microbiology 2004, 70(12): 7110-7118.(并列第一,IF 4.016)

2.    Xiufen Zhou, Xinyi He, Jingdan Liang, Aiying Li, Tiegang Xu, Tobias Kieser, John D. Helmann, and Zixin Deng. A novel DNA modification by sulphur. Molecular Microbiology 2005, 57(5): 1428-1438.(该文荣获2005年中国高校十大科技进展,IF 3.418 )

3.    Xinyi He, Hong-Yu Ou, Qing Yu, Xiufen Zhou, Jun Wu, Jingdan Liang, Wei Zhang, Kumar Rajakumar, and Zixin Deng. Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Molecular Microbiology 2007, 65(4): 1034-1048. (IF 3.418)

4.    Li Li, Zhinan Xu, Xiaoying Xu, Jun Wu, Yun Zhang, Xinyi He*, T. Mark Zabriskie, and Zixin Deng. The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5'-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. ChemBioChem 2008, 9(8): 1286-1294.(IF 2.576)

5.    Guang Liu, Hong-Yu Ou, Tao Wang, Li Li, Huarong Tan, Xiufen Zhou, Kumar Rajakumar, Zixin Deng*, and Xinyi He*. Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLoS Genetics 2010, 6(12): e1001253.(IF5.174)

6.    Jiang Wang, Yi Yu, Kexuan Tang, Wen Liu, Xinyi He*, Xi Huang*, Z. Deng. Identification and analysis of the biosynthetic gene cluster encoding the thiopeptide antibiotic cyclothiazomycin in Streptomyces hygroscopicus 10-22. Applied and Environmental Microbiology 2010, 76(7): 2335-2344.(IF 4.016)

7.    Jun Wu, Li Li, Zixin Deng, T. Mark Zabriskie, and Xinyi He*. Analysis of the mildiomycin biosynthesis gene cluster in Streptoverticillum remofaciens ZJU5119 and characterization of MilC, a hydroxymethyl cytosyl-glucuronic acid synthase. ChemBioChem 2012, 13(11): 1613-1621. (IF 2.576)

8.    Qing Yu, Aiqin Du, Tiangang Liu, Zixin Deng, and Xinyi He*. The biosynthesis of the polyether antibiotic nanchangmycin is controlled by two pathway-specific transcriptional activators. Archives of Microbiology 2012, 194(6): 415-426. (IF 1.884)

9.    Jun Feng, Jun Wu, Nan Dai, Shuangjun Lin, H. Howard Xu, Zixin Deng, and Xinyi He*. Discovery and characterization of BlsE, a radical S-Adenosyl-L-methionine decarboxylase involved in the blasticidin S biosynthetic pathway. PLos One 2013, 8(7): e68545.(IF 2.740)

10.  Chen, C.; Gao, T.; Zhao, G.; Deng, Z.; Hu, S.; Xu, H.H.; He, X. Evidence from 18O feeding studies for hydroxyl group donor in the reaction catalyzed by cytidylate hydroxymethylase MilA. Chinese Science Bulletin 2013, 58, 864-868(IF 9.511)

11.  Li Li, Jun Wu, Zixin Deng, T. Mark Zabriskie, Xinyi He*. Streptomyces lividans blasticidin S deaminase and its application in engineering a blasticidin S-producing strain for ease of genetic manipulation. Applied and Environmental Microbiology 2013, 79(7): 2349-2357. (IF 4.016)

12.  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. (IF 4.016)

13. 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. (IF 11.501)

14.  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. (IF 11.501)

15.  Guiyang Yu, Li Li, Xiangyang Liu, Guang Liu, Zixin Deng, Mark T. Zabriskie, Ming Jiang, and Xinyi He*. The standalone aminopeptidase PepN catalyzes the maturation of blasticidin S from leucylblasticidin S. Scientific Reports 2015, 5: 17641. (IF 3.998)

16.  Daofeng Dai, Aiqin Du, Kangli Xiong, Tianning Pu, Xiufen Zhou, Zixin Deng, Jingdan Liang, Xinyi He*, and Zhijun Wang*. DNA phosphorothioate modification plays a role in peroxides resistance in Streptomyces lividans. Frontiers in Microbiology 2016, 7: 1380. (IF 4.235)

17.  Gong Zhao, Cheng Chen, Wei Xiong, Tuling Gao, Zixin Deng, Geng Wu, and Xinyi He*. Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis. Scientific Reports 2016, 6: 39675. (IF 3.998)

18. 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. (IF 4.235)

19. 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. Mol Microbiol. 2018 Nov;110(3):484-497. (IF 3.418)

20. 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. Nat Commun. 2018 Nov 8;9(1):4689. (IF 12.121)

21. 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 Res. 2019 Aug 22;47(14):7690-7702. (IF 11.501)

22. 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 Res. 2020 Sep 4;48(15):8755-8766. (IF 11.501)

中文文章:

1.    杜爱芹, 吴俊, 邓子新, 贺新义. 杀稻瘟菌素生物合成基因簇的边界确定。 微生物学通报 2014(07): 1318-1325.

2.    高土玲, 陈诚, 赵功, 邓子新, 胡申才, 贺新义。 CMP 羟甲基化酶 MilA 中与甲基羟化过程相关的关键氨基酸定点突变分析. 微生物学通报 2014(01): 50-57.

3.    徐玉松, 高土玲, 于昊, 邓子新, 贺新义。亚硝基胍消除链霉菌FR-008的线性质粒. 微生物学通报 2017(01): 141-149.

4.   贺惠,禹贵阳,邓子新,贺新义。氨肽酶PepN1在细胞外催化杀稻瘟菌素的成熟. 微生物学通报 2019,46(2): 223-232-149.

5.  张丽娜,罗祥坤,邓子新,贺新义。变铅青链霉菌体内游离胞嘧啶的发现及检测. 微生物学通报 2020,46(2): 223-232-149.

 

申请专利:

1. 米多霉素生物合成基因簇,专利号CN200910056338.8,授权日期:2011.07.20

2. 一种目标RNA单碱基编辑的系统和方法,专利号202011120174.3,申请时间:2020.10.19。

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