Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1998 Dec 1;17(23):7139–7148. doi: 10.1093/emboj/17.23.7139

ATP-dependent aggregation of single-stranded DNA by a bacterial SMC homodimer.

M Hirano 1, T Hirano 1
PMCID: PMC1171060  PMID: 9843517

Abstract

SMC (structural maintenance of chromosomes) proteins are putative ATPases that are highly conserved among Bacteria, Archaea and Eucarya. Eukaryotic SMC proteins are implicated in a diverse range of chromosome dynamics including chromosome condensation, dosage compensation and recombinational repair. In eukaryotes, two different SMC proteins form a heterodimer, which in turn acts as the core component of a large protein complex. Despite recent progress, no ATP-dependent activity has been found in individual SMC subunits. We report here the first biochemical characterization of a bacterial SMC protein from Bacillus subtilis. Unlike eukaryotic versions, the B.subtilis SMC protein (BsSMC) is a simple homodimer with no associated subunits. It binds preferentially to single-stranded DNA (ssDNA) and has a ssDNA-stimulated ATPase activity. In the presence of ATP, BsSMC forms large nucleoprotein aggregates in a ssDNA-specific manner. Proteolytic cleavage of BsSMC is changed upon binding to ATP and ssDNA. The energy-dependent aggregation of ssDNA might represent a primitive type of chromosome condensation that occurs during segregation of bacterial chromosomes.

Full Text

The Full Text of this article is available as a PDF (527.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Blattner F. R., Plunkett G., 3rd, Bloch C. A., Perna N. T., Burland V., Riley M., Collado-Vides J., Glasner J. D., Rode C. K., Mayhew G. F. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453–1462. doi: 10.1126/science.277.5331.1453. [DOI] [PubMed] [Google Scholar]
  2. Bode J., Kohwi Y., Dickinson L., Joh T., Klehr D., Mielke C., Kohwi-Shigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science. 1992 Jan 10;255(5041):195–197. doi: 10.1126/science.1553545. [DOI] [PubMed] [Google Scholar]
  3. Britton R. A., Lin D. C., Grossman A. D. Characterization of a prokaryotic SMC protein involved in chromosome partitioning. Genes Dev. 1998 May 1;12(9):1254–1259. doi: 10.1101/gad.12.9.1254. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. doi: 10.1126/science.273.5278.1058. [DOI] [PubMed] [Google Scholar]
  5. Chuang P. T., Albertson D. G., Meyer B. J. DPY-27:a chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome. Cell. 1994 Nov 4;79(3):459–474. doi: 10.1016/0092-8674(94)90255-0. [DOI] [PubMed] [Google Scholar]
  6. Cole S. T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S. V., Eiglmeier K., Gas S., Barry C. E., 3rd Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998 Jun 11;393(6685):537–544. doi: 10.1038/31159. [DOI] [PubMed] [Google Scholar]
  7. Falk G., Walker J. E. DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors. Biochem J. 1988 Aug 15;254(1):109–122. doi: 10.1042/bj2540109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A., Merrick J. M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  9. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. doi: 10.1126/science.270.5235.397. [DOI] [PubMed] [Google Scholar]
  10. Guacci V., Koshland D., Strunnikov A. A direct link between sister chromatid cohesion and chromosome condensation revealed through the analysis of MCD1 in S. cerevisiae. Cell. 1997 Oct 3;91(1):47–57. doi: 10.1016/s0092-8674(01)80008-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B. C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 1996 Nov 15;24(22):4420–4449. doi: 10.1093/nar/24.22.4420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hirano T., Kobayashi R., Hirano M. Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein. Cell. 1997 May 16;89(4):511–521. doi: 10.1016/s0092-8674(00)80233-0. [DOI] [PubMed] [Google Scholar]
  13. Hirano T., Mitchison T. J. A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro. Cell. 1994 Nov 4;79(3):449–458. doi: 10.1016/0092-8674(94)90254-2. [DOI] [PubMed] [Google Scholar]
  14. Hirano T. SMC protein complexes and higher-order chromosome dynamics. Curr Opin Cell Biol. 1998 Jun;10(3):317–322. doi: 10.1016/s0955-0674(98)80006-9. [DOI] [PubMed] [Google Scholar]
  15. Jessberger R., Frei C., Gasser S. M. Chromosome dynamics: the SMC protein family. Curr Opin Genet Dev. 1998 Apr;8(2):254–259. doi: 10.1016/s0959-437x(98)80149-4. [DOI] [PubMed] [Google Scholar]
  16. Jessberger R., Riwar B., Baechtold H., Akhmedov A. T. SMC proteins constitute two subunits of the mammalian recombination complex RC-1. EMBO J. 1996 Aug 1;15(15):4061–4068. [PMC free article] [PubMed] [Google Scholar]
  17. Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996 Jun 30;3(3):109–136. doi: 10.1093/dnares/3.3.109. [DOI] [PubMed] [Google Scholar]
  18. Kimura K., Hirano T. ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation. Cell. 1997 Aug 22;90(4):625–634. doi: 10.1016/s0092-8674(00)80524-3. [DOI] [PubMed] [Google Scholar]
  19. Klenk H. P., Clayton R. A., Tomb J. F., White O., Nelson K. E., Ketchum K. A., Dodson R. J., Gwinn M., Hickey E. K., Peterson J. D. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997 Nov 27;390(6658):364–370. doi: 10.1038/37052. [DOI] [PubMed] [Google Scholar]
  20. Koshland D., Strunnikov A. Mitotic chromosome condensation. Annu Rev Cell Dev Biol. 1996;12:305–333. doi: 10.1146/annurev.cellbio.12.1.305. [DOI] [PubMed] [Google Scholar]
  21. Kowalczykowski S. C., Eggleston A. K. Homologous pairing and DNA strand-exchange proteins. Annu Rev Biochem. 1994;63:991–1043. doi: 10.1146/annurev.bi.63.070194.005015. [DOI] [PubMed] [Google Scholar]
  22. Kunst F., Ogasawara N., Moszer I., Albertini A. M., Alloni G., Azevedo V., Bertero M. G., Bessières P., Bolotin A., Borchert S. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997 Nov 20;390(6657):249–256. doi: 10.1038/36786. [DOI] [PubMed] [Google Scholar]
  23. Lieb J. D., Albrecht M. R., Chuang P. T., Meyer B. J. MIX-1: an essential component of the C. elegans mitotic machinery executes X chromosome dosage compensation. Cell. 1998 Jan 23;92(2):265–277. doi: 10.1016/s0092-8674(00)80920-4. [DOI] [PubMed] [Google Scholar]
  24. Lin D. C., Grossman A. D. Identification and characterization of a bacterial chromosome partitioning site. Cell. 1998 Mar 6;92(5):675–685. doi: 10.1016/s0092-8674(00)81135-6. [DOI] [PubMed] [Google Scholar]
  25. Losada A., Hirano M., Hirano T. Identification of Xenopus SMC protein complexes required for sister chromatid cohesion. Genes Dev. 1998 Jul 1;12(13):1986–1997. doi: 10.1101/gad.12.13.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science. 1991 May 24;252(5009):1162–1164. doi: 10.1126/science.252.5009.1162. [DOI] [PubMed] [Google Scholar]
  27. Matson S. W., Kaiser-Rogers K. A. DNA helicases. Annu Rev Biochem. 1990;59:289–329. doi: 10.1146/annurev.bi.59.070190.001445. [DOI] [PubMed] [Google Scholar]
  28. Michaelis C., Ciosk R., Nasmyth K. Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell. 1997 Oct 3;91(1):35–45. doi: 10.1016/s0092-8674(01)80007-6. [DOI] [PubMed] [Google Scholar]
  29. Moriya S., Tsujikawa E., Hassan A. K., Asai K., Kodama T., Ogasawara N. A Bacillus subtilis gene-encoding protein homologous to eukaryotic SMC motor protein is necessary for chromosome partition. Mol Microbiol. 1998 Jul;29(1):179–187. doi: 10.1046/j.1365-2958.1998.00919.x. [DOI] [PubMed] [Google Scholar]
  30. Munakata N., Morohoshi F., Saitou M., Yamazaki N., Hayashi K. Molecular characterization of thirteen gyrA mutations conferring nalidixic acid resistance in Bacillus subtilis. Mol Gen Genet. 1994 Jul 8;244(1):97–103. doi: 10.1007/BF00280192. [DOI] [PubMed] [Google Scholar]
  31. Notarnicola S. M., McIntosh M. A., Wise K. S. A Mycoplasma hyorhinis protein with sequence similarities to nucleotide-binding enzymes. Gene. 1991 Jan 2;97(1):77–85. doi: 10.1016/0378-1119(91)90012-z. [DOI] [PubMed] [Google Scholar]
  32. Oguro A., Kakeshita H., Honda K., Takamatsu H., Nakamura K., Yamane K. srb: a Bacillus subtilis gene encoding a homologue of the alpha-subunit of the mammalian signal recognition particle receptor. DNA Res. 1995;2(2):95–100. doi: 10.1093/dnares/2.2.95. [DOI] [PubMed] [Google Scholar]
  33. Pettijohn D. E. Structure and properties of the bacterial nucleoid. Cell. 1982 Oct;30(3):667–669. doi: 10.1016/0092-8674(82)90269-0. [DOI] [PubMed] [Google Scholar]
  34. Rao R., Pagan J., Senior A. E. Directed mutagenesis of the strongly conserved lysine 175 in the proposed nucleotide-binding domain of alpha-subunit from Escherichia coli F1-ATPase. J Biol Chem. 1988 Nov 5;263(31):15957–15963. [PubMed] [Google Scholar]
  35. Saitoh N., Goldberg I. G., Wood E. R., Earnshaw W. C. ScII: an abundant chromosome scaffold protein is a member of a family of putative ATPases with an unusual predicted tertiary structure. J Cell Biol. 1994 Oct;127(2):303–318. doi: 10.1083/jcb.127.2.303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Saka Y., Sutani T., Yamashita Y., Saitoh S., Takeuchi M., Nakaseko Y., Yanagida M. Fission yeast cut3 and cut14, members of a ubiquitous protein family, are required for chromosome condensation and segregation in mitosis. EMBO J. 1994 Oct 17;13(20):4938–4952. doi: 10.1002/j.1460-2075.1994.tb06821.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Siegel L. M., Monty K. J. Determination of molecular weights and frictional ratios of proteins in impure systems by use of gel filtration and density gradient centrifugation. Application to crude preparations of sulfite and hydroxylamine reductases. Biochim Biophys Acta. 1966 Feb 7;112(2):346–362. doi: 10.1016/0926-6585(66)90333-5. [DOI] [PubMed] [Google Scholar]
  38. Strunnikov A. V., Hogan E., Koshland D. SMC2, a Saccharomyces cerevisiae gene essential for chromosome segregation and condensation, defines a subgroup within the SMC family. Genes Dev. 1995 Mar 1;9(5):587–599. doi: 10.1101/gad.9.5.587. [DOI] [PubMed] [Google Scholar]
  39. Strunnikov A. V., Larionov V. L., Koshland D. SMC1: an essential yeast gene encoding a putative head-rod-tail protein is required for nuclear division and defines a new ubiquitous protein family. J Cell Biol. 1993 Dec;123(6 Pt 2):1635–1648. doi: 10.1083/jcb.123.6.1635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sutani T., Yanagida M. DNA renaturation activity of the SMC complex implicated in chromosome condensation. Nature. 1997 Aug 21;388(6644):798–801. doi: 10.1038/42062. [DOI] [PubMed] [Google Scholar]
  41. Tsang S. S., Chow S. A., Radding C. M. Networks of DNA and RecA protein are intermediates in homologous pairing. Biochemistry. 1985 Jun 18;24(13):3226–3232. doi: 10.1021/bi00334a023. [DOI] [PubMed] [Google Scholar]
  42. Weinstock G. M., McEntee K., Lehman I. R. ATP-dependent renaturation of DNA catalyzed by the recA protein of Escherichia coli. Proc Natl Acad Sci U S A. 1979 Jan;76(1):126–130. doi: 10.1073/pnas.76.1.126. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES