叶克穷博士 - 科学研究 - 北京生命科学研究所

叶克穷博士

北京生命科学研究所高级研究员

Keqiong Ye, Ph.D. Associate Investigator, NIBS, Beijing, China

Phone：010-80726688-8550

Fax： 010-80728592

E-mail：yekeqiong@nibs.ac.cn

教育经历

Education

1995	浙江大学生物学学士
	B.S., Department of Biological Science and Technology,Zhejiang University, Hangzhou, China.
2000	中科院生物物理所博士
	Ph.D., Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China (Dr. Jinfeng Wang)

工作经历

Professional Experience

2011-	北京生命科学研究所高级研究员 Associate Investigator, National Institute of Biological Sciences, Beijing.
2005-2011	北京生命科学研究所研究员
	Assistant Investigator, National Institute of Biological Sciences, Beijing.
2001-2005	斯隆癌症研究所博士后
	Postdoc with Dr. Dinshaw J. Patel. Memorial Sloan-Kettering Cancer Center, New York, USA.

研究概述：

我们实验室主要研究蛋白质和核糖核酸之间的相互作用。核糖核酸除了在基因表达中作为信使,还行使许多其他的功能。在各种生物体中已经发现了很多非编码的核糖核酸，它们不翻译成蛋白质，却在分子结构，反应催化，基因调节中发挥重要作用。这些非编码核糖核酸通常和蛋白质形成复合物行使功能。实验室主要的研究领域包括核酸干扰，这是由长度约为21个核甘酸的微小核糖核酸介导的基因调控过程。我们实验室将研究这些微小核酸生物发生机理，工作原理和调控途径。我们还研究由核糖核酸引导的核糖核酸修饰系统，如催化核糖甲基化的C/D RNP和假尿嘧啶化的H/ACA RNP。实验室主要使用X光晶体学，核磁共振等结构方法以及生化分析作为研究手段。

Research Description:

Our laboratory mainly studies interactions between protein and RNA. RNAs play diverse roles in cells in addition to their roles in gene expression. A large number of non-coding RNAs that are never translated into protein have been identified in various organisms. Non-coding RNAs function as structural, catalytic and regulatory molecules and frequently work in collaboration with proteins by forming RNA protein complexes (RNPs). One of our major interest is RNA silencing (popularly known as RNAi), where small RNAs of about 21 nucleotides in length guide gene regulation. Work on this topic is concerned with understanding small RNA generation, function and regulation. Our lab is also interested in the structure and function of RNA-guided RNA modification enzymes, namely box C/D and H/ACA RNPs that direct ribose 2'-o-methylation and pseudouridylation, respectively. Structural approaches such as x-ray crystallography and NMR, combined with biochemical techniques, are used to study these problems.

Publications：

1. Sanduo Zheng#, Pengfei Lan#, Ximing Liu and Keqiong Ye*(2014) Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast. J. Biol. Chem. doi:10.1074/jbc.M114.584490, July 2, 2014

2. Sanduo Zheng and Keqiong Ye* (2014) Purification, crystallization and preliminary X-ray diffraction analysis of Imp3 in complex with an Mpp10 peptide involved in yeast ribosome biogenesis. Acta Cryst. F90, 918-921

3. Dejian Zhou, Keqiong Ye* (2014) CLIP techniques in studying protein-RNA interactions. Chinese Bulletin of Life Sciences 26(3) 207-212

4. Cheng Zhang, Jinzhong Lin, Weixiao Liu, Xining Chen, Rongchang Chen and Keqiong Ye*(2014) Structure of Utp21 tandem WD domain provides insight into the organization of the UTPB complex involved in ribosome synthesis. PLoS ONE 9(1): e86540. doi:10.1371/journal.pone.0086540 Jan 21, 2014

5. Jing Lu, Mengyi Sun and Keqiong Ye*(2013) Structural and functional analysis of Utp23, a yeast ribosome synthesis factor with degenerate PIN domain. RNA. 19:1815-24. doi:10.1261/rna.040808.113 Dec 1, 2013

6. Jinzhong Lin#, Jing Lu#, Yingang Feng, Mengyi Sun and Keqiong Ye*(2013) An RNA-binding complex involved in ribosome biogenesis contains a protein with homology to tRNA CCA-adding enzyme. PLoS Biol 11(10): e1001669. doi:1001610.1001371/journal.pbio.1001669.

7. Jie Zheng, Lei Zhang, Junbin Zhang, Xiaoxia Wang, Keqiong Ye ,Zhen Xi*, Quan Du*, Zicai Liang* (2013) Single modification at position 14 of siRNA strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. FASEB J. 10:4017-26. doi: 10.1096/fj.13-228668. 2013 Jun 14.

8. Yue-He Ding#, Yun-Guang Du#, Shukun Luo#, Yu-Xin Li, Tie-Mei Li, Sawako Yoshina, Xing Wang, Karsten Klage, Shohei Mitani, Keqiong Ye* , Meng-Qiu Dong* (2013) Characterization of PUD-1 and PUD-2, Two Proteins Up-Regulated in a Long-Lived daf-2 Mutant. PLoS ONE 8(6):e67158. doi: 10.1371/journal.pone.0067158. 2013 Jun 14

9. Liman Zhang, Jinzhong Lin and Keqiong Ye (2013) Structural and functional analysis of the U3 snoRNA binding protein Rrp9. RNA doi: 10.1261/rna.037580.112, Mar. 18, 2013

10. Sanduo Zheng#, Jia Wang#, Yingang Feng#,*, Jinfeng Wang andKeqiong Ye* (2012) Solution structure of MSL2 CXC domain reveals an unusual Zn3Cys9 cluster and similarity to pre-SET domains of histone lysine methyltransferases. PLoS ONE, 7(9):e45437. doi: 10.1371/journal.pone.0045437

11. Xinxing Yang, Jinqi Duan, Shuang Li, Peng Wang, Shoucai Ma, Keqiong Ye* and Xin Sheng Zhao* (2012) Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation. Nucleic Acids Res. 40:10925-36. doi: 10.1093/nar/gks882

12. Bing Yang#, Yan-Jie Wu#, Ming Zhu#, Sheng-Bo Fan, Jinzhong Lin, Kun Zhang, Shuang Li, Hao Chi, Yu-Xin Li, Hai-Feng Chen, Shu-Kun Luo, Yue-He Ding, Le-Heng Wang, Zhiqi Hao, Li-Yun Xiu, She Chen, Keqiong Ye, Si-Min He* and Meng-Qiu Dong* (2012) Identification of cross-linked peptides from complex samples. Nature Method. 9:904-906. doi:10.1038/nmeth.2099

13. Xing Zhu and Keqiong Ye (2012) Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. FEBS Letters. 10.1016/j.febslet.2012.02.036.

14. Wei Zhang, Yang Zhao, Yan Guo and Keqiong Ye (2012) Plant actin-binding protein SCAB1 is dimeric actin cross-linker with atypical pleckstrin homology domain. J. Biol. Chem. doi:10.1074/jbc.M112.341347.

15. Shukun Luo and Keqiong Ye (2012) Dimerization, but not phosphothreonine binding, is conserved between the forkhead-associated domains of Drosophila MU2 and human MDC1. FEBS Letters. 586:344-349. doi:10.1016/j.febslet.2012.01.023.

16. Jinping Liu^#, Shukun Luo^#, Hongchang Zhao, Ji Liao, Jing Li, Chunying Yang, Bo Xu, David F. Stern, Xingzhi Xu* and Keqiong Ye* (2012) Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain. Nucleic Acids Res. doi:10.1093/nar/gkr1296 (^#equal contribution, *corresponding author)

17. Shuang Li, Jingqi Duan, Dandan Li, Shoucai Ma and Keqiong Ye 2011.Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. EMBO J. doi:10.1038/emboj.2011.427

18.Shuang Li, Jingqi Duan, Dandan Li, Bing Yang, Mengqiu Dong and Keqiong Ye 2011. Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase. Genes Dev 25: 2409-2421. doi:10.1101/gad.175299.111

19.Jinzhong Lin, Liman Zhang, Shaomei Lai, Keqiong Ye. 2011 Structure and molecular evolution of CDGSH iron-sulfur domains. PLoS ONE, 6(9): e24790. doi:10.1371/journal.pone.0024790

20.Yang Zhao, Shuangshuang Zhao, Tonglin Mao, Xiaolu Qu, Wanhong Cao, Li Zhang, Wei Zhang, Liu He, Sidi Li, Sulin Ren, Jinfeng Zhao, Guoli Zhu, Shanjin Huang, Keqiong Ye, Ming Yuan, and Yan Guo. 2011 The Plant-Specific Actin Binding Protein SCAB1 Stabilizes Actin Filaments and Regulates Stomatal Movement in Arabidopsis. Plant Cell. doi:10.1105/tpc.111.086546

21.Bihong Guo, Jinzhong Lin and Keqiong Ye. 2011. Structure of the autocatalytic cysteine protease domain of potyvirus helper-component proteinase. J. Biol. Chem. 286: 21937-21943 doi:10.1074/jbc.M111.230706

22. Lin J., Lai S., Jia R., Xu A., Zhang L.,Lu J. and Ye K. 2011 Structural basis of site-specific ribose methylation by box C/D RNA protein complexes.Nature 469: 559-563

23. Huang L., Yin P., Zhu X., Zhang Y. and Ye K. 2010 Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100. Nucleic Acids Res. doi:10.1093/nar/gkq915

24. Shen M., Xu Y., Jia R., Zhou X. and Ye K. 2010 Size-independent and non-cooperative recognition of dsRNA by the Rice stripe virus RNA silencing suppressor NS3. J Mol Biol. 404: 665-679

25. Ye K., Jia R., Lin J., Ju M., Peng J., Xu A. and Zhang L. 2009 Structural organization of box C/D RNA-guided RNA methyltransferase. Proc Natl Acad Sci USA, 106: 13808-13813

26. Duan J., Li L., Lu J., Wang W. and Ye K. 2009. Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.Mol Cell. 34:427-439

27. Lin J, Zhou T, Ye K, Wang J. Crystal structure of human mitoNEET reveals distinct groups of iron sulfur proteins. PNAS. 2007 104(37):14640-5.

28. Ye, K. 2007. H/ACA guide RNAs, proteins and complexes. Current Opinion in Structural Biology. 2007, 17:287–292

29. Li, L. and Ye, K. 2006. Crystal structure of an H/ACA box ribonucleoprotein particle. Nature 443: 302-307.

30. Ye K. and Patel D.J.. RNA silencing suppressor p21 of Beet Yellows Virus forms an RNA-binding octameric ring structure. Structure. 2005; 13, 1375-1384.

31. *Ma J., *Ye K. and Patel D.J.. Structural mechanism of overhang-specific small interfering RNA recognition of the PAZ domain. Nature. 2004; 429:318-322. (*Equal contribution)

32. Ye K., Malinina L. and Patel D.J.. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature. 2003; 426:874-878.

33. Ye K., Serganov A., Hu W., Garber M. and Patel D.J.. Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur. J. Biochem. 2002; 269:5182-5191.

34. Ye K. and Wang J.. Self-association reaction of denatured staphylococcal nuclease fragments characterized by heteronuclear NMR. J. Mol. Biol.2001; 307:309-322.

35. Ye K., Jing G. and Wang J.. Interactions between subdomains in the partially folded state of staphylococcal nuclease. Biochim. Biophys. Acta.2000; 1479:123-134.