The National Institute of Diabetes & Digestive & Kidney Diseases

The objective of our research is to gain detailed mechanistic insights into the cellular processes that impact the genomic structure and the heritance of the genomic material. The genomes of all organisms are under the threat of assault by transposable elements. We study the mechanism of DNA transposition of the bacteriophage Mu as a model system of a wide family of DNA rearrangement reactions from bacteria to humans. These reactions are involved in a variety of processes that impact our health, from spread of drug resistance among pathogenic bacteria to replication of retroviruses such as HIV. The immunoglobulin gene rearrangement reaction in vertebrates also takes place by a closely related mechanism. We use biochemical, molecular biological, and biophysical approaches including single-molecule techniques for our studies. We have made advances in our understanding of the reaction steps and the chemical mechanisms involved in these reactions. Our recent efforts center around the understanding of the assembly and disassembly dynamics of the macromolecular complexes involved in these reactions by developing and utilizing single-molecule biochemical approaches.

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

1. Greene EC, Mizuuchi K Visualizing the assembly and disassembly mechanisms of the MuB transposition targeting complex. J Biol Chem (279): 16736-43, 2004. [Full Text/Abstract]

2. Yanagihara K, Mizuuchi K Progressive structural transitions within Mu transpositional complexes. Mol Cell (11): 215-24, 2003. [Full Text/Abstract]

3. Hoskins JR, Yanagihara K, Mizuuchi K, Wickner S ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence. Proc Natl Acad Sci U S A (99): 11037-42, 2002. [Full Text/Abstract]

4. Greene EC, Mizuuchi K Direct observation of single MuB polymers: evidence for a DNA-dependent conformational change for generating an active target complex. Mol Cell (9): 1079-89, 2002. [Full Text/Abstract]

5. Greene EC, Mizuuchi K Dynamics of a protein polymer: the assembly and disassembly pathways of the MuB transposition target complex. EMBO J (21): 1477-86, 2002. [Full Text/Abstract]

6. Yanagihara K, Mizuuchi K Mismatch-targeted transposition of Mu: a new strategy to map genetic polymorphism. Proc Natl Acad Sci U S A (99): 11317-21, 2002. [Full Text/Abstract]

7. Greene EC, Mizuuchi K Target immunity during Mu DNA transposition. Transpososome assembly and DNA looping enhance MuA-mediated disassembly of the MuB target complex. Mol Cell (10): 1367-78, 2002. [Full Text/Abstract]

8. Mizuuchi M, Mizuuchi K Conformational isomerization in phage Mu transpososome assembly: effects of the transpositional enhancer and of MuB. EMBO J (20): 6927-35, 2001. [Full Text/Abstract]

9. Zheng R, Ghirlando R, Lee MS, Mizuuchi K, Krause M, Craigie R Barrier-to-autointegration factor (BAF) bridges DNA in a discrete, higher-order nucleoprotein complex. Proc Natl Acad Sci U S A (97): 8997-9002, 2000. [Full Text/Abstract]

10. Kennedy AK, Haniford DB, Mizuuchi K Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: insights from phosphorothioate stereoselectivity. Cell (101): 295-305, 2000. [Full Text/Abstract]

11. Mizuuchi K, Nobbs TJ, Halford SE, Adzuma K, Qin J A new method for determining the stereochemistry of DNA cleavage reactions: application to the SfiI and HpaII restriction endonucleases and to the MuA transposase. Biochemistry (38): 4640-8, 1999. [Full Text/Abstract]

12. Wei SQ, Mizuuchi K, Craigie R Footprints on the viral DNA ends in moloney murine leukemia virus preintegration complexes reflect a specific association with integrase. Proc Natl Acad Sci U S A (95): 10535-40, 1998. [Full Text/Abstract]

13. 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]

14. Mizuuchi K Polynucleotidyl transfer reactions in site-specific DNA recombination. Genes Cells (2): 1-12, 1997. [Full Text/Abstract]

15. Yang W, Mizuuchi K Site-specific recombination in plane view. Structure (5): 1401-6, 1997. [Full Text/Abstract]

16. Clubb RT, Schumacher S, Mizuuchi K, Gronenborn AM, Clore GM Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase. J Mol Biol (273): 19-25, 1997. [Full Text/Abstract]

17. Schumacher S, Clubb RT, Cai M, Mizuuchi K, Clore GM, Gronenborn AM Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains. EMBO J (16): 7532-41, 1997. [Full Text/Abstract]

18. Rice PA, Yang S, Mizuuchi K, Nash HA Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell (87): 1295-306, 1996. [Full Text/Abstract]

19. Savilahti H Mizuuchi K Mu transpositional recombination: donor DNA cleavage and strand transfer in trans by the Mu transposase. Cell(85): 271-80, 1996. [Full Text/Abstract]

20. van Gent DC, Mizuuchi K, Gellert M Similarities between initiation of V(D)J recombination and retroviral integration. Science (271): 1592-4, 1996. [Full Text/Abstract]

21. Mizuuchi M Baker TA Mizuuchi K Assembly of phage Mu transpososomes: cooperative transitions assisted by protein and DNA scaffolds. Cell(83): 375-85, 1995. [Full Text/Abstract]

22. Rice P Mizuuchi K Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell(82): 209-20, 1995. [Full Text/Abstract]