再访刘一 连发Nature Cell非易事 解决问题是关键

　　

编者按：5月14日的《Nature》杂志以封面文章形式发表了德克萨斯大学西南医学中心刘一的一篇RNAi研究前沿文章，不久后，刘一教授再度在《Cell》杂志上发表生物昼夜节律分子机理研究成果文章。记者再度连线刘一教授，了解刘一教授的最新动态。

 

在这篇Cell文章中，刘一教授首次研究真核生物昼夜节律的转录后调节机制，为揭开转录后调节环路打开了一扇窗。

具体见生物通前期报道：

专访RNAi前沿科学家刘一 《Nature》封面文章作者

刘一《Nature》封面 解析新型RNAi分子

刘一《Cell》文章 继《Nature》封面文章后又一力作

 

 

生物通记者：我发现您这篇Cell文章和上次的Nature文章都是以脉孢菌为模型的，选择它有什么特别的理由吗？

 

刘一教授：的确，我的两篇文章都是选择脉孢菌做模型动物的，不同的是Nature的那篇文章是研究RNAi的，而Cell的这篇文章是研究生物昼夜节律的。选择脉孢菌的原因在于，它是一个优秀的真核生物模型，它具有另一个真核生物模型裂殖酵母所没有的一些生物特征而这些生物特征在高等真核生物中也存在。比如说，昼夜节律和RNAi现象，尽管真菌与动物在进化枝上的距离较远，但是在昼夜节律方面和RNAi方面却惊人的相似。因此说，我们以脉孢菌为模型研究昼夜节律是具有普遍生物学意义的。

生物通记者：昼夜节律的研究对生命科学有什么重要的意义？

 

刘一教授：部分原核生物和大部分的真核生物都具有昼夜节律这一生物特征，包括人类在内，昼夜节律机制控制着生命体的多种分子和生理活动。对人类和哺乳动物而言，昼夜节律控制着很多生命活动，如，睡眠生物钟，体温循环系统，内分泌系统，以及基因的活性等等。了解昼夜节律的机制有助我们了解更多的生命活动的调节过程。

 

 

生物通记者：您的这篇Cell文章主要解开了昼夜节律调节的哪些问题？具有什么样的意义？

 

刘一教授：以往的研究发现昼夜节律内源性的节律控制环路所控制，这个环路包括一个负反馈环路。在以往的研究中，科学家们对这个负反馈环路的认识主要停留在转录的水平上，转录后的调控机制知道的很少。

 

在我们的研究中，通过用脉孢菌作为模型，我们发现了一个新的转录后的负反馈回路，这个回路的组成与转录水平上的回路相似，但是它们不像转录水平回路影响mRNA的转录而是影响mRNA的稳定性。这个回路主要结合 核心节律调控因子和exosome(在真核生物中调节mRNA稳定性的关键因子）来发挥作用。

 

此外，我们还发现exosome的某些核心物质的表达是受昼夜节律所调控的，这些表达对昼夜节律的调节具有重要的意义，并且还受一些节律基因的调控。我们的研究发现了昼夜节律调节机制的一个重要部分，并且我们发现转录水平上的调节和转录后调节在昼夜节律方面具有同等重要的意义。

 

生物通记者：您的实验室主要研究RNAi和昼夜节律，这两个课题看似没有太大的关联，为什么您会选择这两个课题？

 

刘一教授：是的，这两个领域看似没有太大的关联，也并不相似，不过研究这两个领域都用得上遗传和生化系统模型，而刚好脉孢菌具备这一切的优势。RNAi和昼夜节律都是真核生物系统的重要研究领域。

生物通记者：在研究过程中您主要应用哪些生物技术？您的实验过程中有用哪些新技术吗，尤其是有对实验结果至关重要的技术吗？

 

刘一教授：大部分都是通用型的技术，不过，有时候为了研究的需要，我们会自己整合分子生物学技术和生化技术或是遗传学技术，用于我们特定需求的研究目的。

生物通记者：您下一步将进行哪些方面的研究？

 

刘一教授：我们将进一步研究转录后水平的昼夜节律调控以及转录后水平调控对昼夜节律的影响。这仅仅是我们研究昼夜节律的一部分，我们还将继续研究转录水平上和转录后水平上的昼夜节律调控机制。

 

生物通记者：您在短短的几个月内就连着发表了一篇Nature封面文章和Cell文章，能在这两种顶级的杂志上发文章都不容易，对于发表文章您有什么心得？

 

刘一教授：我认为在这两个杂志上发文章的确不容易，不过我认为在做研究的过程中，研究者应该坚持解答生命科学现象中的重要的问题。

 

我建议生命科学研究者关注核心的问题，并且深入系统的进行分析，这样就会得出重要的结论，重要的是我们的研究解决了生命科学中的重要问题，文章发在哪并不是那么重要。

 

后记

生物通记者有幸两度采访刘一教授，不得不感叹刘一教授对科学研究的专注和发表文章的速度，可以说每一份专注都换来了成绩，然而这背后的坚持和辛苦确是从文章难以看出的。我们祝福刘一教授，也期待他有更好的成绩。

（生物通 张欢）

刘一简介

 

EDUCATION:

 

8/1990-8/1995               Ph.D. Vanderbilt University, Nashville, TN.  Advisor: Dr. Carl H. Johnson. Dissertation: Molecular mechanism of circadian clock in cyanobacteria.

 

9/1985-7/1989              B.S. Wuhan University, Wuhan, Hubei, China.

 

 

PROFESSIONAL EXPERIENCE:

 

9/2008-present      Professor, University of Texas Southwestern Medical Center, Dallas, TX

 

2008-2013             Editorial Board Member, Journal of Biological Chemistry

 

3/2006-3/2010               Elected Neurospora Policy Committee member. Scientific Chair of the 2008 Neurospora Meeting.

 

7/2005-present               Chairman of the Integrative Biology Graduate Program

 

9/2004                          Associate Professor, University of Texas Southwestern Medical Center, Dallas, TX

 

9/1999-8/2004               Assistant Professor and Louise W. Kahn Endowed Scholar in Biomedical Research and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX

 

9/1995-9/1999              Postdoctoral Research Associate with Dr. Jay Dunlap,                                          Department of Biochemistry, Dartmouth Medical School, Hanover, NH.

 

9/1990-5/1995         Teaching Assistant, Department of Biology, Vanderbilt University.

 

 

FELLOWSHIPS AND AWARDS:

 

3/2004                          The Beadle and Tatum Award, The Neurospora policy committee. Given to one researcher every two years for outstanding contribution using Neurospora as a model system.

 

1999-2003                     Louise W. Kahn Endowed Scholar in Biomedical Research

 

8/1998-9/1999               NIH National Research Service Award for Individual Postdoctoral Fellows. Grant Number: 1F32 GM19230-01.

 

9/1990-8/1995              Vanderbilt University Graduate Fellowship and Tuition Fellowship.

 

7/1995                          Best Conference Abstract Award, American Physiologist Society

 

9/1994                          Vanderbilt University Ph.D. Dissertation Enhancement Award.

 

 

Current Grants:

 

NIH, R01 GM068496 Posttranscriptional Regulation of the Neurospora Circadian Clock, 8/1/03-7/31/11. Direct cost: $210,000/year.

 

NIH, R01 GM062591 Molecular Mechanism of the Neurospora Circadian Clock, 2/1/01-

1/31/10. Direct cost: $200,000/year.

 

NIH, RO1 GM084283 Double-stranded RNA-mediated signaling pathway and gene silencing. Funding expected 4/1/09. $180,000/year

 

Welch Foundation, Biochemical analysis of COP9 signalosome, 6/1/03-5/31/09. Direct cost: $50,000/year.

 

UT Southwestern High Risk/High Impact grant, 2007-2008. $75,000

Welch Foundation, Biochemical analysis of COP9 signalosome, 6/1/03-5/31/09. Direct cost: $50,000/year.

 

 

Teaching:

 

Chairman of the Integrative Biology Graduate Program, 7/2005-present

 

Co-organizer of the Integrative Biology weekly Works in Progress (9/2005-present)

 

Organizing the Integrative Biology Journal Clubs, 9/2005-present

Currently, there are six interest-based journal clubs (Cancer, Metabolism, Diabetes, CNS Diseases, Cardiac, Human Genetics)

 

Coordinator of the Cells & Organelles literature Critique seession of the DCMB Core course, 2003-present. Responsible for recruiting faculty discussion leaders, selecting papers and providing paper guidelines.

 

Lectured in the Response to Stress course (on How environment entrains circadian clock): 2000-present.

 

Lectured in the Cell signaling course (on the Molecular mechanism of circadian clock): 2005-present.

 

 

 

PUBLICATIONS:

 

1. Liu, Y., S.S. Golden, T. Kondo, M. Ishiura, and C.H. Johnson. (1995) Bacterial luciferase as a reporter of circadian gene expression in cyanobacteria.  J. Bacteriology 177:2080-2086.

 

2. Liu, Y., N.F. Tsinoremas, C.H. Johnson, N.V. Lebedeva, S.S. Golden, M. Ishiura, and T. Kondo. (1995) Circadian orchestration of gene expression in cyanobacteria. Genes & Development  9:1469-1478.

 

3. Liu , Y. and N.F. Tsinoremas. (1996) Unusual gene arrangement for the putative chromosome replication origin and circadian gene expression of dnaN gene in Synechococcus sp. strain PCC 7942. Gene 172 (1):105-109.

 

4. Liu, Y., N.F. Tsinoremas, S.S. Golden, T. Kondo, and C.H. Johnson. (1996) Circadian expression of genes involved in the de novo purine biosynthetic pathway of cyanobacteria.  Molecular Microbiology  20 (5): 1071-1081.

 

5. Garceau, N.C., Y. Liu, J.J. Loros, and J.C. Dunlap. (1997) Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY. Cell 89:469-476

 

6. Liu, Y., N.Y. Garceau, J.J. Loros, and J.C. Dunlap. (1997) Thermally regulated translational control of the frequency protein mediates aspects of temperature responses in the Neurospora circadian clock.  Cell 89: 477-486. (subject of a mini review in Cell).

 

7. Dunlap, J. C., J.J. Loros, S.K.Crosthwaite, Y. Liu  et al.,  (1998) The circadian regulatory system in Neurospora. In Light and Time in Microbial Systems, D. Roberts, ed. (Cambridge: Cambridge Univ. Press).

 

8. Liu, Y., M. Merrow, J.J. Loros, and J.C. Dunlap. (1998) How temperature changes reset a circadian oscillator.  Science 281:825-829.

 

9. Dunlap, J.C., J.J. Loros, Y. Liu, and S.K. Crosthwaite(1999) Eukaryotic circadian systems: cycles in common.  Genes to Cells 4:1-10.

 

10. Liu, Y., C. Heintzen, J.J. Loros, and J.C. Dunlap. (1999) Regulation of clock genes. Cell. Mol. Life Sci. 55:1195-1205.

 

11. Liu, Y., J.J. Loros, and J.C.Dunlap (2000). Phosphorylation of the Neurospora clock protein FREQUENCY determines its degradation rate and strongly influences the period length of the circadian clock. Proc. Natl. Acad. Sci. USA 97: 234-239.

 

12. Cheng, P, Y. Yang, C. Heintzen, and Y. Liu (2001) Coiled-coil domain mediated FRQ-FRQ interaction is essential for its circadian clock function in Neurospora.  EMBO J.  20: 101-108.

 

13. Cheng, P, Y. Yang, and Y. Liu. (2001) Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock. Proc. Natl. Acad. Sci. USA 98:7408-7413

 

14. Yang, Y., P. Cheng, G. Zhi, and Y. Liu (2001) Identification of a calcium/calmodulin-dependent protein kinase that phosphorylates the Neurospora circadian clock protein FREQUENCY. J. Biol. Chem. 276: 41064-41072

 

15. Cheng, P, Y. Yang, K. H. Gardner, and Y. Liu. (2002)  PAS domain mediated WC-1/WC-2 heterodimeric complex is essential for their circadian clock function and the stability of WC-1. Mol. Cell. Biol  22: 517-524

 

16. Yang, Y., P. Cheng, and Y. Liu. (2002) Regulation of the Neurospora circadian clock by casein kinase II. Genes & Development  15:994-1006.

 

17. He, Q.*, P. Cheng*, Y. Yang, L. Wang, K. H. Gardner, and Y. Liu. (2002)  White Collar-1, a DNA-binding transcription factor and a light sensor. Science. 297: 840-843 (cover article, accompanied by a Perspective)

 

18. Froehlich, A. C., Y. Liu, J. J. Loros, and J. C. Dunlap.  (2002) White Collar-1, a circadian blue light photoreceptor, binds to the frequency promoter. Science. 297: 815-819 843 (cover article, accompanied by Perspective)

 

19. Cheng, P, Y. Yang, L, Wang, Q. He, and Y. Liu. (2003) WHITE COLLAR-1, a multifunctional Neurospora protein involved in the circadian feedback loops, light sensing, and transcription repression of wc-2.  J. Biol. Chem.  278:3801-3808.

 

20. Cheng, P., Q. He, Y. Yang, L, Wang, and Y. Liu. (2003)  Functional conservation of light, oxygen, or voltage domains in light sensing.  Proc. Natl. Acad. Sci. USA 100:5938-5943

 

21. Liu, Y., (2003) J. Biol. Rhythms  Molecular mechanisms of entrainment of the Neurospora circadian clock.  18: 195-205.

 

22. Yang, Y., P. Cheng, Q. He, L. Wang, and Y. Liu  (2003) Phosphorylation of FREQUENCY Protein by Casein Kinase II is Necessary for the Function of the Neurospora Circadian Clock.  Mol. Cell. Biol  23:6221-6228

 

23. He, Q.*, Cheng, P.*, Y. Yang, Q. He, H. Yu, and Y. Liu. (2003) FWD1-mediated degradation of FREQUENCY in Neurospora establishes a conserved mechanism for circadian clock regulation.  EMBO J. 22:4421-4430

 

24. Liu, Y., Q. He, and P. Cheng. (2003) Photoreception in Neurospora, A Tale of Two White Collar Proteins.   Cell. Mol. Life Sci.  60:2131-2138.

 

25. Yang, Y., Q. He, P. Cheng, P. Wrage, Oded Yarden, and Y. Liu. (2004) Distinct roles for PP1 and PP2A in the Neurospora circadian clock. Genes & Development. 18:255-260

 

26. Min, H., Y. Liu, C. H. Johnson, and S. S. Golden. (2004) Phase Determination of Circadian Gene Expression in Synechococcus elongatus PCC 7942.  J. Biol. Rhythms  19:103-112.

 

27. Liu, Y., Y. Yang. and Q. He (2005) Posttranscriptional regulation of the Neurospora circadian clock. In “Circadian Clocks in Eukaryotic Microbes”. Edited by Fred Kippert. published by Landes Bioscience. (http://www.eurekah.com/abstract.php?chapid=2329&bookid=180&catid=85&PHPSESSID=4ca3afca5fc5f5d6da4e00fcc7abc154)

 

28. Liu, Y.(2005)  Analysis of posttranslational regulations in the Neurospora circadian clock. Methods in Enzymology. “Circadian Rhythms”,Edited by Michael Young.  393:379-393

 

29. Cheng, P., Q. He, Q. He, L. Wang, and Y. Liu.  (2005) Regulation of the Neurospora circadian clock by an RNA helicase. Genes & Development  19: 234-241.

 

30. He Q., H. Shu, P. Cheng, S. Chen, L. Wang, and Y. Liu. (2005) Light-independent phosphorylation of WHITE COLLAR-1 is important for its role in the circadian negative feedback loop.  J. Biol. Chem. 280: 17526-17532.

 

31. He, Q., Cheng, P., Q. He, and Y. Liu. (2005) The COP9 signalosome regulates the Neurospora circadian clock by controlling the stability of the SCFFWD-1 complex.  Genes & Development 19: 1518-1531.

 

32. He, Q, and Y. Liu (2005) Degradation of the Neurospora circadian clock protein FREQUENCY through the ubiquitin-proteasome pathway. Biochem Soc Trans. 33:953-956.

 

33. He, Q. and Y. Liu (2005) Molecular mechanism of light responses in Neurospora: from light-induced transcription to photoadaptation. Genes & Development 19: 2888-2899.

 

34. Huang, G., L. Wang, and Y. Liu (2006) Molecular mechanism of suppression of circadian rhythm by a critical stimulus. EMBO J.  25: 5349-5357.

 

35. Liu. Y. and D. Bell-Pedersen (2006) Circadian rhythms in Neurospora and other filamentous fungi. Eukaryotic Cell. 5: 1184-1193.

 

36. He, Q., J. Cha, Q. He, H. Lee, Y. Yang, and Y. Liu. (2006) CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop. Genes & Dev. 20:2552-2565.

 

37. Heintzen, C. and Y. Liu (2007) The Neurospora crassa circadian clock. Adv in Genetics, 58:25-66

 

38. Maiti, M., HC. Lee, and Y. Liu (2007) QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes & Dev. 21: 590-600

 

39. Choudhary, S.*, HC Lee*, M. Maiti*, Q. He, P. Cheng, Q. Liu, and Y. Liu (2007) A double-stranded RNA response program important for RNAi efficiency. Mol. Cell. Biol. 27:3995-4005. (the cover article).

 

40. Guocun Huang, She Chen, Shaojie Li, Joonseok Cha, Chengzu Long, Lily Li, Qiyang He and Yi Liu. (2007) Protein Kinase A and Casein Kinases Mediate Sequential Phosphorylation Events in the Circadian Negative Feedback Loop. Genes & Dev. 21: 3283-3295.

 

41. Cha, J., G. Huang, J. Guo, and Y. Liu (2007) Posttranslational control of the Neurospora circadian clock. Cold Spring Harbor Symposia on Quantitative Biology 72: 185-91.

 

42. Cha J, Chang SS, Huang G, Cheng P, and Y. Liu (2008) Control of WHITE COLLAR localization by phosphorylation is a critical step in the circadian negative feedback process. EMBO J. 27: 3246-3255.

 

43. He Q., Tang C, and Y. Liu (2008) The roles of the ubiquitin-proteasome system in the control of circadian clocks. The Ubiquitin Proteasome System. Edited by Napoli and Wojcik. In press.

 

44. Jinhu Guo, Guocun Huang, Joonseok Cha, Yi Liu (2008) Protein analyses of the filamentous fungus Neurospora crassa. Molecular and Cell Biology Methods for Fungi. Edited by Amir Sharon. In press.

 

45. Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH, Y. Liu. (2009) qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459(7244):274-277.

 

46. Chi-Tai Tang, Shaojie Li, Chengzu Long,  Joonseok Cha, Guocun Huang, Lily Li, She Chen and Yi Liu (2009) Setting the pace of the Neurospora circadian clock by multiple independent FRQ phosphorylation events. Proc. Natl. Acad. Sci. USA (in press).