Lab Research Interests:

 We investigate the mechanism of the Escherichia coli condensin MukBEF. The core of this complex, MukB, belongs to the family of SMC (structural maintenance of chromosome) protein, which were implicated in virtually every event that affects the higher order chromatin structure. MukF is a kleisin. MukF forms a stable complex with MukE, MukEF, which can further associate with MukB. MukBEF is required for faithful chromosome organization and segregation in E. coli. Mutational inactivation of MukBEF results in chromosome decondensation and cutting and increased production of anucleate cells.

What do we think:
MukBEF is the protein that organizes chromosomes into the looped structures.
 

How do we study MukBEF:

1. Biochemistry
 

Fig. 1. Purified MukB promotes formation of DNA knots, which can be detected by gel electrophoresis or electron microscopy. DNA knotting rather than catenation signals that the protein supports intramolecular DNA condensation.

2. Cell Biology
 

Fig. 2. Overproduced MukBEF and MukB rapidly condense chromosomes. Size bar, 5 mm.

3. Single DNA Enzymology
 

Fig. 3. Condensation of a single DNA molecule by MukB can be observed using Magnetic Tweezers. A number of single condensation events can be found on the trace.

 
 

Nucleus can speed up quantification of the size and subcellular localization of spots in bacteria. Nucleus is designed for high throughput analysis of fluorescence micrographs. Version 1 of the program still has a few flaws and only reduces, not eliminates the observer’s bias. The Figure on the right illustrates spot recognition by Nucleus. The program can be downloaded for non-commercial use from the link below. If you find the program useful, please cite: Wang, Q.et al. “Chromosome condensation in the absence of non-SMC subunits of MukBEF.” J. Bacteriol., (2006) 188(12):4431-41 . Download NUCLEUS

 

Selected Publications:

Rybenkov, V.V., Cozzarelli, N.R. and Vologodskii, A.V., "The probability of DNA knotting and the effective diameter of the DNA double helix." Proc. Natl. Acad. Sci. USA, 90, 5307-5311, 1993.

Rybenkov, V.V., Vologodskii, A.V. and Cozzarelli, N.R., "The effect of ionic conditions on conformations of supercoiled DNA. I Sedimentation analysis." J. Mol. Biol., 267, 299-311, 1997.

Rybenkov, V.V., Vologodskii, A.V. and Cozzarelli, N.R., "The effect of ionic conditions on conformations of supercoiled DNA. II Catenation equilibrium." J. Mol. Biol., 267, 312-323, 1997.

Rybenkov, V.V., Vologodskii, A.V. and Cozzarelli, N.R., "The effect of ionic conditions on DNA helical repeat, effective diameter, and free energy of supercoiling" Nucl. Acids Res., 25, 1412-1418, 1997.

Rybenkov, V.V., Ullsperger, C. U., Vologodskii, A.V. and Cozzarelli, N.R., "Simplification of DNA topology below equilibrium values by type II topoisomerases." Science, 277, 690-693, 1997.

Alexandrov, A.I., Cozzarelli N.R., Holmes, V.F., Khodursky, A.B., Peter, B.J., Postow, L., Rybenkov, V.V. and Vologodskii, A.V. "Mechanisms of separation of the complementary strands of DNA during replication." in "Structural Biology and Functional Genomics", NATO Science Series 3 (High technology), E. Morton Bradbury and Sandor Pongor (eds), Kluwer Academic Publishers, Dordrecht, Boston, London, 1999, pp. 217-235.

Kimura, K., Rybenkov, V.V., Crisona, N., Hirano, T. and Cozzarelli, N.R. "13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation" Cell, 98 (2), 239-248, 1999.

Vologodskii, A.V., Zhang, W., Rybenkov, V.V., Podtelezhnikov, A.A., Subramanian, D., Griffith, J.D., Cozzarelli, N.R. "Mechanism of topology simplification by type II DNA topoisomerases", Proc. Natl. Acad. Sci., 98(6), 3045-3049, 2001.

Dekker, N.H., Rybenkov, V.V., Duguet, M., Cozzarelli, N.R., Bensimon, D. “The Mechanism of Type IA Topoisomerases” Proc. Natl. Acad. Sci. USA, (2002) 99(19):12126-31.

Petrushenko, Z.M., Lai, C., Rai, R., Rybenkov, V.V. “DNA reshaping by MukB: right-handed knotting, left-handed supercoiling” J. Biol. Chem., (2006) 281(8):4606-15.

Wang, Q., Mordukhova, E., Edwards A., Rybenkov, V.V. “Chromosome condensation in the absence of non-SMC subunits of MukBEF.” J. Bacteriol., (2006) 188(12):4431-41.

Petrushenko, Z.M., Lai, C., Rybenkov, V.V. “Antagonistic interaction between kleisins and DNA with bacterial condensin MukB” J. Biol. Chem., (2006).

She, W., Wang, Q., Mordukhova, E.A. and Rybenkov, V.V. “MukEF is required for stable association of MukB with the chromosome” submitted 2006