Scientists&Research
Keqiong Ye, Ph.D.
- Information
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- Experience
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Keqiong Ye, Ph.D.
Associate Investigator, NIBS, Beijing, China
Phone:010-80726688-8550
Fax: 010-80728592
E-mail:yekeqiong@nibs.ac.cn
Education
1995 |
B.S., Department of Biological Science and Technology, |
2000 |
Ph.D., Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China (Dr. Jinfeng Wang) |
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Professional Experience
2011- |
Associate Investigator, National Institute of Biological Sciences, Beijing.
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2005-2011 |
Assistant Investigator, National Institute of Biological Sciences, Beijing. |
2001-2005 |
Postdoc with Dr. Dinshaw J. Patel. Memorial Sloan-Kettering Cancer Center, New York, USA. |
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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.