教育背景

博士: 1993.8-1996.12,英国伯明翰大学University of Birmingham (UK),分子与细胞生物学

硕士: 1986.9-1989.6,兰州大学,植物生态学

本科1982.9-1986.6,兰州大学,植物学

工作经历

2003.11-现在:山东大学微生物技术国家重点实验室,教授,博导

1999.4-2003.10:日本通产省产业技术综合研究所,研究员

1997.1-1999.3:日本农水省果树研究所,博士后（STA特别研究员）

1989.7-1993.8:中国农业科学院兰州畜牧研究所，助理研究员

研究方向

1.极端环境微生物资源、嗜酸热微生物合成生物学及极端酶

2.古菌DNA损伤响应与DNA修复

2.硫化叶菌细胞分裂、病毒出芽及囊泡分泌

3.硫化叶菌细胞周期调控

研究内容

古菌和真核生物拥有共同的祖先，硫化叶菌（Sulfolobus）生长于80°C以上、pH3-5的高温、酸性环境，其遗传信息传递机制、细胞周期调控与真核生物十分接近。同时，硫化叶菌也是许多古菌病毒的宿主。因此，硫化叶菌是研究古菌DNA代谢、细胞周期和病毒与宿主相互作用最为常用的模式微生物。本课题组主要开展古菌及其病毒的基础及应用基础研究。主要利用硫化叶菌开展如下工作：（1）以嗜酸热古菌硫化叶菌作为底盘细胞，开展合成生物学和极端酶的基础与应用研究；（2）鉴定硫化叶菌DNA修复蛋白的生化性质、结构、体内功能；（3）分析硫化叶菌以ESCRT-III为基础的细胞分裂、膜泡释放和囊膜病毒（STSV2）的出芽过程；（4）解析腾冲硫化叶菌STSV2病毒与宿主的相互作用；（4）研究硫化叶菌周期的调控机制。研究目标是构建可高效降解生物质、生产生物燃料和化学品的新型合成生物学底盘细胞；揭示古菌DNA修复、细胞分裂、病毒外排和细胞周期调控的分子机制，为真核生物的相关研究提供启示，并为嗜酸热底盘细胞的改造提供理论基础。

主讲课程

极端环境微生物学及其专题讲座

招生信息

招生专业:生物化学与分子生物学、微生物学

每年招收硕士、博士研究生数名,欢迎有志于科学研究的学子们踊跃报考。另外课题组招收博士后若干名，欢迎有分子生物学、代谢工程等生物学相关专业博士生加入团队。

正在承担及已完成科研项目：

1.国家自然科学基金面上项目,硫化叶菌新型错配修复蛋白EndoMS的生化性质鉴定与体内功能的遗传分析, 2020-01至2023-12。

2.科技部国家重点研发计划“极端微生物底盘细胞的设计与构建”子课题：耐热、耐酸微生物底盘细胞的设计构建与表征，2020-07至2025-06。

3.国家自然科学基金面上项目,冰岛硫化叶菌新型ATP酶PINA的生化性质与结构及其在同源重组修复中的作用研究, 2017-1至2020-12。

4.国家自然科学基金面上项目，硫化叶菌Holliday junction解离酶Hje的体内功能与作用机制研究，2015-1至2018-12。

5.国家自然科学基金面上项目，超嗜热古菌Sulfolobus islandicus核酸切除修复途径研究，2012-1至2015-12。

6.国家自然科学基金重点项目，超嗜热古菌DNA重组修复解旋酶和核酸酶的作用机制及体内功能，2010-1至2013-12。

7.国家自然科学基金面上项目，古菌Hjm解旋酶参与复制叉回退和Holliday junction加工的机制，2009-1至2011-12。

8.国家自然科学基金面上项目，超嗜热古菌Pyrococcus horikoshii几丁质降解酶研究，2006-1至2008-12。

9.国家重点基础研究发展（973）计划子课题,极端嗜热古菌DNA修复与重组机制，2004-9至2009-8。

10.国家自然科学基金面上项目，超嗜热古菌DNA复制、修复及重组酶的研究，2005-1至2007-12。

主要论文

Liu, J., Cvirkaite-Krupovic, V., Baquero, D.P., Yang, Y., Zhang, Q., Shen, Y.*, and Krupovic, M*. (2021). Virus-induced cell gigantism and asymmetric cell division in Archaea. Proc Natl Acad Sci USA, 118(15): e2022578118.

Liu, J., Cvirkaite-Krupovic, V., Commere, P., Yang, Y., Zhou, F., Forterre, P., Shen, Y., and Krupovic, M*. (2021b). Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments. The ISME J, doi: 10.1038/s41396-021-00984-0.

Ahmad, S., Huang, Q., Ni, J., Xiao, Y., Yang, Y.,Shen, Y.*(2020). Functional Analysis of the NucS/EndoMS of the Hyperthermophilic Archaeon Sulfolobus islandicus REY15A. Front Microbiol11, 607431.

Huang, Q., Lin, Z., Wu, P., Ni, J.,Shen, Y.*(2020). Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A. Front Microbiol11, 586025.

Huang, Q., Mayaka, J.B., Zhong, Q., Zhang, C., Hou, G., Ni, J.,Shen, Y.*(2019). Phosphorylation of the Archaeal Holliday Junction Resolvase Hjc Inhibits Its Catalytic Activity and Facilitates DNA Repair in Sulfolobus islandicus REY15A. Front Microbiol10, 1214.

Mayaka, J.B., Huang, Q., Xiao, Y., Zhong, Q., Ni, J.,Shen, Y.*(2019). The Lonely Guy (LOG) Homologue SiRe_0427 from the Thermophilic Archaeon Sulfolobus islandicus REY15A Is a Phosphoribohydrolase Representing a Novel Group. Appl Environ Microbiol85.

Zhai, B., DuPrez, K., Han, X., Yuan, Z., Ahmad, S., Xu, C., Gu, L., Ni, J., Fan, L.*,Shen, Y.*(2018). The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction. Nucleic Acids Res46, 6627-6641.

Liu, J., Gao, R., Li, C., Ni, J., Yang, Z., Zhang, Q., Chen, H.,Shen, Y.*(2017). Functional assignment of multiple ESCRT-III homologs in cell division and budding in Sulfolobus islandicus. Mol Microbiol105, 540-553.

Huang, Q., Zhong, Q., Mayaka, J.B.A., Ni, J.,Shen, Y.*(2017). Autophosphorylation and Cross-Phosphorylation of Protein Kinases from the Crenarchaeon Sulfolobus islandicus. Front Microbiol8, 2173.

Yan, Z., Yuan, Z., Ni, J., Gu, L.,Shen, Y.*(2017). Crystal structure of the crenarchaeal ExoIII AP endonuclease SisExoIII reveals a conserved disulfide bond endowing the protein with thermostability. Biochem Biophys Res Commun490, 774-779.

Zhai, B., DuPrez, K., Doukov, T.I., Li, H., Huang, M., Shang, G., Ni, J., Gu, L.,Shen, Y.*, and Fan, L*. (2017). Structure and Function of a Novel ATPase that Interacts with Holliday Junction Resolvase Hjc and Promotes Branch Migration. J Mol Biol429, 1009-1029.

Yan, Z., Huang, Q., Ni, J.,Shen, Y.*(2016). Distinct catalytic activity and in vivo roles of the ExoIII and EndoIV AP endonucleases from Sulfolobus islandicus. Extremophiles20, 785-793.

Song, X., Huang, Q., Ni, J., Yu, Y.,Shen,Y.*(2016a). Knockout and functional analysis of two DExD/H-box family helicase genes in Sulfolobus islandicus REY15A. Extremophiles20, 537-546.

Song, X., Ni, J.,Shen, Y.*(2016b). Structure-Based Genetic Analysis of Hel308a in the Hyperthermophilic Archaeon Sulfolobus islandicus. J Genet Genomics43, 405-413.

Huang, Q., Li, Y., Zeng, C., Song, T., Yan, Z., Ni, J., She, Q*.,Shen, Y.*(2015a). Genetic analysis of the Holliday junction resolvases Hje and Hjc in Sulfolobus islandicus. Extremophiles19, 505-514.

Huang, Q., Liu, L., Liu, J., Ni, J., She, Q*.,Shen, Y.*(2015b). Efficient 5'-3' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus. BMC Mol Biol16, 2.

Liang, P.J., Han, W.Y., Huang, Q.H., Li, Y.Z., Ni, J.F., She, Q.X.,Shen, Y.*. (2013). Knockouts of RecA-like proteins RadC1 and RadC2 have distinct responses to DNA damage agents in Sulfolobus islandicus. J Genet Genomics40, 533-542.

Hong, Y., Chu, M., Li, Y., Ni, J., Sheng, D., Hou, G., She, Q.,Shen, Y.*(2012). Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair (Amst)11, 102-111.

Wang, L., Sheng, D., Han, W., Huang, B., Zhu, S., Ni, J., Li, J.,Shen, Y.*(2012). Sulfolobus tokodaii RadA paralog, stRadC2, is involved in DNA recombination via interaction with RadA and Hjc. Sci China Life Sci55, 261-267.

Zheng, T., Huang, Q., Zhang, C., Ni, J., She, Q.,Shen, Y.*(2012). Development of a simvastatin selection marker for a hyperthermophilic acidophile, Sulfolobus islandicus. Appl Environ Microbiol78, 568-574.

Ma, X., Hong, Y., Han, W., Sheng, D., Ni, J., Hou, G.,Shen, Y.*(2011). Single-stranded DNA binding activity of XPBI, but not XPBII, from Sulfolobus tokodaii causes double-stranded DNA melting. Extremophiles15, 67-76.

Wei, T., Zhang, S., Hou, L., Ni, J., Sheng, D.,Shen, Y.*(2011). The carboxyl terminal of the archaeal nuclease NurA is involved in the interaction with single-stranded DNA-binding protein and dimer formation. Extremophiles15, 227-234.

Li, Z., Lu, S., Hou, G., Ma, X., Sheng, D., Ni, J.,Shen, Y.*(2008). Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. J Bacteriol190, 3006-3017.

Lu, S., Li, Z., Wang, Z., Ma, X., Sheng, D., Ni, J.,Shen, Y.*(2008). Spatial subunit distribution and in vitro functions of the novel trimeric PCNA complex from Sulfolobus tokodaii. Biochem Biophys Res Commun376, 369-374.

Wei, T., Zhang, S., Zhu, S., Sheng, D., Ni, J.,Shen, Y.*(2008). Physical and functional interaction between archaeal single-stranded DNA-binding protein and the 5'-3' nuclease NurA. Biochem Biophys Res Commun367, 523-529.

Zhang, S., Wei, T., Hou, G., Zhang, C., Liang, P., Ni, J., Sheng, D.,Shen, Y.*(2008). Archaeal DNA helicase HerA interacts with Mre11 homologue and unwinds blunt-ended double-stranded DNA and recombination intermediates. DNA Repair (Amst)7, 380-391.

Sheng, D., Li, M., Jiao, J., Ni, J.,Shen, Y.*(2008a). Co-expression with RadA and the characterization of stRad55B, a RadA paralog from the hyperthermophilic crenarchaea Sulfolobus tokodaii. Sci China C Life Sci51, 60-65.

Sheng, D., Zhu, S., Li, M., Jiao, J., Ni, J.,Shen, Y.* (2008b). [Cloning, expression and radiation inducibility of RadA from the hyperthermophilic archaeon Sulfolobus tokodaii]. Wei Sheng Wu Xue Bao48, 317-322.

Sheng, D., Zhu, S., Wei, T., Ni, J.,Shen, Y.*(2008c). The in vitro activity of a Rad55 homologue from Sulfolobus tokodaii, a candidate mediator in RadA-catalyzed homologous recombination. Extremophiles12, 147-157.

Liu, B., Hong, Y., Wu, L., Li, Z., Ni, J., Sheng, D.,Shen, Y.*(2007). A unique highly thermostable 2-phosphoglycerate forming glycerate kinase from the hyperthermophilic archaeon Pyrococcus horikoshii: gene cloning, expression and characterization. Extremophiles11, 733-739.

Shen, Y.*,Tang, X.F., Matsui, E., and Matsui, I. (2004). Subunit interaction and regulation of activity through terminal domains of the family D DNA polymerase from Pyrococcus horikoshii. Biochem Soc Trans32, 245-249.

Shen, Y.*,Tang, X.F., Yokoyama, H., Matsui, E., and Matsui, I. (2004). A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor. Nucleic Acids Res32, 158-168.

Shen, Y.*,Tang, X.F., and Matsui, I. (2003). Subunit interaction and regulation of activity through terminal domains of the family D DNA polymerase from Pyrococcus horikoshii. J Biol Chem278, 21247-21257.

Shen, Y.*, Musti, K., Hiramoto, M., Kikuchi, H., Kawarabayashi, Y., and Matsui, I. (2001). Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii. J Biol Chem276, 27376-27383.