Structural and functional similarities between two bacterial chromosome compacting machineries

Biochemical and Biophysical Research Communications

Volumn 386, Issue 3, 2009, Pages 415-419

  Lim, Jae Hong ^a   Oh, Byung Ha ^b  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

^b Center for Biomolecular Recognition   (South Korea)

Author keywords

Chromosome condensation; Condensin; MukB; MukE; MukF; Nucleoid; Protein structure; ScpA; ScpB; SMC

Indexed keywords

CONDENSIN; PROTEIN MUKB; PROTEIN MUKE; PROTEIN MUKF; PROTEIN SCPA; PROTEIN SCPB; PROTEIN SMC; UNCLASSIFIED DRUG;

BACTERIAL CHROMOSOME; CHROMOSOME CONDENSATION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; SHORT SURVEY;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CELL CYCLE PROTEINS; CHROMOSOMES, BACTERIAL; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 67650069252     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2009.06.019     Document Type: Short Survey

References (38)

1. Woldringh C.L., and Nanninga N. Structure of nucleoid and cytoplasm in the intact cell. In: Nanninga N. (Ed). Molecular Cytology of Escherichia coli (1985), Academic Press, London, England 161-197
2. Zimmerman S.B. Shape and compaction of Escherichia coli nucleoids. J. Struct. Biol. 156 (2006) 255-261
3. Tolstorukov M.Y., Virnik K.M., Adhya S., and Zhurkin V.B. A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res. 33 (2005) 3907-3918
4. Zimmerman S.B., and Murphy L.D. Macromolecular crowding and the mandatory condensation of DNA in bacteria. FEBS Lett. 390 (1996) 245-248
5. Holmes V.F., and Cozzarelli N.R. Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling. Proc. Natl. Acad. Sci. USA 97 (2000) 1322-1324
6. Thanbichler M., and Shapiro L. Chromosome organization and segregation in bacteria. J. Struct. Biol. 156 (2006) 292-303
7. Cobbe N., and Heck M.M. The evolution of SMC proteins: phylogenetic analysis and structural implications. Mol. Biol. Evol. 21 (2004) 332-347
8. Graumann P.L. SMC proteins in bacteria: condensation motors for chromosome segregation?. Biochimie 83 (2001) 53-59
9. Losada A., and Hirano T. Dynamic molecular linkers of the genome: the first decade of SMC proteins. Genes Dev. 19 (2005) 1269-1287
10. Melby T.E., Ciampaglio C.N., Briscoe G., and Erickson H.P. The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge. J. Cell Biol. 142 (1998) 1595-1604
11. Soppa J. Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins. Gene 278 (2001) 253-264
12. Hirano T. At the heart of the chromosome: SMC proteins in action. Nat. Rev. Mol. Cell Biol. 7 (2006) 311-322
13. Nasmyth K., and Haering C.H. The structure and function of SMC and kleisin complexes. Annu. Rev. Biochem. 74 (2005) 595-648
14. Niki H., Jaffe A., Imamura R., Ogura T., and Hiraga S. The new gene mukB codes for a 177 kDa protein with coiled-coil domains involved in chromosome partitioning of E. coli. EMBO J. 10 (1991) 183-193
15. Yamanaka K., Ogura T., Niki H., and Hiraga S. Identification of two new genes, MukE and mukF, involved in chromosome partitioning in Escherichia coli. Mol. Gen. Genet. 250 (1996) 241-251
16. Yamazoe M., Onogi T., Sunako Y., Niki H., Yamanaka K., Ichimura T., and Hiraga S. Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli. EMBO J. 18 (1999) 5873-5884
17. Mascarenhas J., Soppa J., Strunnikov A.V., and Graumann P.L. Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein. EMBO J. 21 (2002) 3108-3118
18. Soppa J., Kobayashi K., Noirot-Gros M.F., Oesterhelt D., Ehrlich S.D., Dervyn E., Ogasawara N., and Moriya S. Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol. Microbiol. 45 (2002) 59-71
19. Woo J.S., Lim J.H., Shin H.C., Suh M.K., Ku B., Lee K.H., Joo K., Robinson H., Lee J., Park S.Y., Ha N.C., and Oh B.H. Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions. Cell 136 (2009) 85-96
20. Matoba K., Yamazoe M., Mayanagi K., Morikawa K., and Hiraga S. Comparison of MukB homodimer versus MukBEF complex molecular architectures by electron microscopy reveals a higher-order multimerization. Biochem. Biophys. Res. Commun. 333 (2005) 694-702
21. Lammens A., Schele A., and Hopfner K.P. Structural biochemistry of ATP-driven dimerization and DNA-stimulated activation of SMC ATPases. Curr. Biol. 14 (2004) 1778-1782
22. Hirano M., and Hirano T. ATP-dependent aggregation of single-stranded DNA by a bacterial SMC homodimer. EMBO J. 17 (1998) 7139-7148
23. Niki H., Imamura R., Kitaoka M., Yamanaka K., Ogura T., and Hiraga S. E. coli MukB protein involved in chromosome partition forms a homodimer with a rod-and-hinge structure having DNA binding and ATP/GTP binding activities. EMBO J. 11 (1992) 5101-5109
24. Petrushenko Z.M., Lai C.H., Rai R., and Rybenkov V.V. DNA reshaping by MukB. Right-handed knotting, left-handed supercoiling. J. Biol. Chem. 281 (2006) 4606-4615
25. Volkov A., Mascarenhas J., Andrei-Selmer C., Ulrich H.D., and Graumann P.L. A prokaryotic condensin/cohesin-like complex can actively compact chromosomes from a single position on the nucleoid and binds to DNA as a ring-like structure. Mol. Cell. Biol. 23 (2003) 5638-5650
26. Haering C.H., Lowe J., Hochwagen A., and Nasmyth K. Molecular architecture of SMC proteins and the yeast cohesin complex. Mol. Cell 9 (2002) 773-788
27. Gruber S., Arumugam P., Katou Y., Kuglitsch D., Helmhart W., Shirahige K., and Nasmyth K. Evidence that loading of cohesin onto chromosomes involves opening of its SMC hinge. Cell 127 (2006) 523-537
28. Kim J.S., Lee S., Kang B.S., Kim M.H., Lee H.S., and Kim K.J. Crystal structure and domain characterization of ScpB from Mycobacterium tuberculosis. Proteins 71 (2008) 1553-1556
29. Schleiffer A., Kaitna S., Maurer-Stroh S., Glotzer M., Nasmyth K., and Eisenhaber F. Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. Mol. Cell 11 (2003) 571-575
30. Fennell-Fezzie R., Gradia S.D., Akey D., and Berger J.M. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. EMBO J. 24 (2005) 1921-1930
31. Mascarenhas J., Volkov A.V., Rinn C., Schiener J., Guckenberger R., and Graumann P.L. Dynamic assembly, localization and proteolysis of the Bacillus subtilis SMC complex. BMC Cell Biol. 6 (2005) 28
32. Hirano M., and Hirano T. Positive and negative regulation of SMC-DNA interactions by ATP and accessory proteins. EMBO J. 23 (2004) 2664-2673
33. Chen N., Zinchenko A.A., Yoshikawa Y., Araki S., Adachi S., Yamazoe M., Hiraga S., and Yoshikawa K. ATP-induced shrinkage of DNA with MukB protein and the MukBEF complex of Escherichia coli. J. Bacteriol. 190 (2008) 3731-3737
34. Arumugam P., Nishino T., Haering C.H., Gruber S., and Nasmyth K. Cohesin's ATPase activity is stimulated by the C-terminal Winged-helix domain of its kleisin subunit. Curr. Biol. 16 (2006) 1998-2008
35. Danilova O., Reyes-Lamothe R., Pinskaya M., Sherratt D., and Possoz C. MukB colocalizes with the oriC region and is required for organization of the two Escherichia coli chromosome arms into separate cell halves. Mol. Microbiol. 65 (2007) 1485-1492
36. Ohsumi K., Yamazoe M., and Hiraga S. Different localization of SeqA-bound nascent DNA clusters and MukF-MukE-MukB complex in Escherichia coli cells. Mol. Microbiol. 40 (2001) 835-845
37. Rost B., and Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19 (1994) 55-72
38. Deleage G., and Roux B. An algorithm for protein secondary structure prediction based on class prediction. Protein Eng. 1 (1987) 289-294