The National Institute of Diabetes & Digestive & Kidney Diseases

Our research focuses on mechanistic aspects of retroviral DNA integration. After entering the host cell, a DNA copy of the viral genome is made by reverse transcription. Integration of this viral DNA into a chromosome of the host cell is an essential step in the retroviral replication cycle.

The key player in the retroviral DNA integration process is the virally encoded integrase protein. Integrase processes the ends of the viral DNA and covalently inserts these processed ends into host DNA. We study the molecular mechanism of these reactions using biochemical, biophysical and structural techniques. Close collaborations with X-ray crystallography and NMR groups in NIDDK form an integral part of our research.

We also study other aspects of the retroviral DNA integration process in cell culture. Viral DNA made by reverse transcription forms part of a large nucleoprotein complex derived from the core of the infecting virion. These integration complexes, isolated from the cytoplasm of virus-infected cells, efficiently integrate their DNA in vitro with all the hallmarks of the authentic in vivo reaction. In contrast, current in vitro systems using purified integrase protein and simple DNA substrates lack the full fidelity of the in vivo reaction. We are studying integration complexes isolated from infected cells to determine the features that confer this high fidelity.

For more information, see the Site-Specific Recombination site.

1. Williams KL, Zhang Y, Shkriabai N, Karki RG, Nicklaus MC, Kotrikadze N, Hess S, Le Grice SF, Craigie R, Pathak VK, Kvaratskhelia M Mass spectrometric analysis of the HIV-1 integrase-pyridoxal 5''-phosphate complex reveals a new binding site for a nucleotide inhibitor. J Biol Chem (280): 7949-55, 2005. [Full Text/Abstract]

2. Li M, Craigie R Processing of viral DNA ends channels the HIV-1 integration reaction to concerted integration. J Biol Chem (280): 29334-9, 2005. [Full Text/Abstract]

3. Bradley CM, Craigie R Seeing is believing: structure of the catalytic domain of HIV-1 integrase in complex with human LEDGF/p75. Proc Natl Acad Sci U S A (102): 17543-4, 2005. [Full Text/Abstract]

4. Bradley CM, Ronning DR, Ghirlando R, Craigie R, Dyda F Structural basis for DNA bridging by barrier-to-autointegration factor. Nat Struct Mol Biol (12): 935-6, 2005. [Full Text/Abstract]

5. Shkriabai N, Patil SS, Hess S, Budihas SR, Craigie R, Burke TR Jr, Le Grice SF, Kvaratskhelia M Identification of an inhibitor-binding site to HIV-1 integrase with affinity acetylation and mass spectrometry. Proc Natl Acad Sci U S A (101): 6894-9, 2004. [Full Text/Abstract]

6. Suzuki Y, Yang H, Craigie R LAP2alpha and BAF collaborate to organize the Moloney murine leukemia virus preintegration complex. EMBO J (23): 4670-8, 2004. [Full Text/Abstract]

7. Bradley C, Craigie R MoMLV reverse transcriptase regulates its own expression. Cell (115): 250-1, 2003. [Full Text/Abstract]

8. Segura-Totten M, Kowalski AK, Craigie R, Wilson KL Barrier-to-autointegration factor: major roles in chromatin decondensation and nuclear assembly. J Cell Biol (158): 475-85, 2002. [Full Text/Abstract]

9. Suzuki Y, Craigie R Regulatory mechanisms by which barrier-to-autointegration factor blocks autointegration and stimulates intermolecular integration of Moloney murine leukemia virus preintegration complexes. J Virol (76): 12376-80, 2002. [Full Text/Abstract]

10. Wang JY, Ling H, Yang W, Craigie R Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. EMBO J (20): 7333-43, 2001. [Full Text/Abstract]

11. Lee MS Craigie R A previously unidentified host protein protects retroviral DNA from autointegration. Proc Natl Acad Sci U S A (95): 1528-33, 1998. [Full Text/Abstract]

12. Wei SQ Mizuuchi K Craigie R A large nucleoprotein assembly at the ends of the viral DNA mediates retroviral DNA integration. EMBO J (16): 7511-20, 1997. [Full Text/Abstract]

13. Jenkins TM Esposito D Engelman A Craigie R Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-crosslinking. EMBO J (16): 6849-59, 1997. [Full Text/Abstract]

14. Cai M Zheng R Caffrey M Craigie R Clore GM Gronenborn AM Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nat Struct Biol (4): 567-77, 1997. [Full Text/Abstract]

15. Jenkins TM Engelman A Ghirlando R Craigie R A soluble active mutant of HIV-1 integrase: involvement of both the core and carboxyl-terminal domains in multimerization. J Biol Chem (271): 7712-8, 1996. [Full Text/Abstract]