Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Oct 11;21(20):4726–4733. doi: 10.1093/nar/21.20.4726

Cpf1 protein induced bending of yeast centromere DNA element I.

R K Niedenthal 1, M Sen-Gupta 1, A Wilmen 1, J H Hegemann 1
PMCID: PMC331497  PMID: 8233820

Abstract

The centromere complex is a multicomponent structure essential for faithful chromosome transmission. Here we show that the S. cerevisiae centromere protein Cpf1 bends centromere DNA element I (CDEI) with the bend angle ranging from 66 degrees to 71 degrees. CDEI DNA sequences that carry point mutations which lead to reduced Cpf1 binding affinity and in vivo centromere activity are still able to show bending. The Cpf1 induced bend is directed towards the major groove with the bend centre located in CDEI. An intrinsic bend cannot replace the Cpf1 induced DNA bend for in vivo centromere function. An in vivo phasing experiment suggests that both the distance and the correct spatial arrangement of the CDEI/Cpf1 complex to CDEII and CDEIII are important for optimal centromere function.

Full text

PDF
4726

Images in this article

Selected References

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

  1. Baker R. E., Masison D. C. Isolation of the gene encoding the Saccharomyces cerevisiae centromere-binding protein CP1. Mol Cell Biol. 1990 Jun;10(6):2458–2467. doi: 10.1128/mcb.10.6.2458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beckmann H., Su L. K., Kadesch T. TFE3: a helix-loop-helix protein that activates transcription through the immunoglobulin enhancer muE3 motif. Genes Dev. 1990 Feb;4(2):167–179. doi: 10.1101/gad.4.2.167. [DOI] [PubMed] [Google Scholar]
  3. Blackwood E. M., Eisenman R. N. Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science. 1991 Mar 8;251(4998):1211–1217. doi: 10.1126/science.2006410. [DOI] [PubMed] [Google Scholar]
  4. Bloom K., Hill A., Kenna M., Saunders M. The structure of a primitive kinetochore. Trends Biochem Sci. 1989 Jun;14(6):223–227. doi: 10.1016/0968-0004(89)90031-5. [DOI] [PubMed] [Google Scholar]
  5. Bolshoy A., McNamara P., Harrington R. E., Trifonov E. N. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2312–2316. doi: 10.1073/pnas.88.6.2312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bracco L., Kotlarz D., Kolb A., Diekmann S., Buc H. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 1989 Dec 20;8(13):4289–4296. doi: 10.1002/j.1460-2075.1989.tb08615.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bram R. J., Kornberg R. D. Isolation of a Saccharomyces cerevisiae centromere DNA-binding protein, its human homolog, and its possible role as a transcription factor. Mol Cell Biol. 1987 Jan;7(1):403–409. doi: 10.1128/mcb.7.1.403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cai M., Davis R. W. Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy. Cell. 1990 May 4;61(3):437–446. doi: 10.1016/0092-8674(90)90525-j. [DOI] [PubMed] [Google Scholar]
  9. Carbon J., Clarke L. Centromere structure and function in budding and fission yeasts. New Biol. 1990 Jan;2(1):10–19. [PubMed] [Google Scholar]
  10. Carr C. S., Sharp P. A. A helix-loop-helix protein related to the immunoglobulin E box-binding proteins. Mol Cell Biol. 1990 Aug;10(8):4384–4388. doi: 10.1128/mcb.10.8.4384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chen J. W., Evans B., Rosenfeldt H., Jayaram M. Bending-incompetent variants of Flp recombinase mediate strand transfer in half-site recombinations: role of DNA bending in recombination. Gene. 1992 Sep 21;119(1):37–48. doi: 10.1016/0378-1119(92)90064-v. [DOI] [PubMed] [Google Scholar]
  12. Cottarel G., Shero J. H., Hieter P., Hegemann J. H. A 125-base-pair CEN6 DNA fragment is sufficient for complete meiotic and mitotic centromere functions in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Aug;9(8):3342–3349. doi: 10.1128/mcb.9.8.3342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Cumberledge S., Carbon J. Mutational analysis of meiotic and mitotic centromere function in Saccharomyces cerevisiae. Genetics. 1987 Oct;117(2):203–212. doi: 10.1093/genetics/117.2.203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. DePinho R. A., Hatton K. S., Tesfaye A., Yancopoulos G. D., Alt F. W. The human myc gene family: structure and activity of L-myc and an L-myc pseudogene. Genes Dev. 1987 Dec;1(10):1311–1326. doi: 10.1101/gad.1.10.1311. [DOI] [PubMed] [Google Scholar]
  15. Dowell S. J., Tsang J. S., Mellor J. The centromere and promoter factor 1 of yeast contains a dimerisation domain located carboxy-terminal to the bHLH domain. Nucleic Acids Res. 1992 Aug 25;20(16):4229–4236. doi: 10.1093/nar/20.16.4229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ferrari S., Harley V. R., Pontiggia A., Goodfellow P. N., Lovell-Badge R., Bianchi M. E. SRY, like HMG1, recognizes sharp angles in DNA. EMBO J. 1992 Dec;11(12):4497–4506. doi: 10.1002/j.1460-2075.1992.tb05551.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fisher F., Goding C. R. Single amino acid substitutions alter helix-loop-helix protein specificity for bases flanking the core CANNTG motif. EMBO J. 1992 Nov;11(11):4103–4109. doi: 10.1002/j.1460-2075.1992.tb05503.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Funk M., Hegemann J. H., Philippsen P. Chromatin digestion with restriction endonucleases reveals 150-160 bp of protected DNA in the centromere of chromosome XIV in Saccharomyces cerevisiae. Mol Gen Genet. 1989 Oct;219(1-2):153–160. doi: 10.1007/BF00261171. [DOI] [PubMed] [Google Scholar]
  19. Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 1988 Jun 30;333(6176):824–829. doi: 10.1038/333824a0. [DOI] [PubMed] [Google Scholar]
  20. Gaudet A., Fitzgerald-Hayes M. Mutations in CEN3 cause aberrant chromosome segregation during meiosis in Saccharomyces cerevisiae. Genetics. 1989 Mar;121(3):477–489. doi: 10.1093/genetics/121.3.477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Goodman S. D., Nash H. A. Functional replacement of a protein-induced bend in a DNA recombination site. Nature. 1989 Sep 21;341(6239):251–254. doi: 10.1038/341251a0. [DOI] [PubMed] [Google Scholar]
  22. Gregor P. D., Sawadogo M., Roeder R. G. The adenovirus major late transcription factor USF is a member of the helix-loop-helix group of regulatory proteins and binds to DNA as a dimer. Genes Dev. 1990 Oct;4(10):1730–1740. doi: 10.1101/gad.4.10.1730. [DOI] [PubMed] [Google Scholar]
  23. Harrington R. E. DNA curving and bending in protein-DNA recognition. Mol Microbiol. 1992 Sep;6(18):2549–2555. doi: 10.1111/j.1365-2958.1992.tb01431.x. [DOI] [PubMed] [Google Scholar]
  24. Hegemann J. H., Fleig U. N. The centromere of budding yeast. Bioessays. 1993 Jul;15(7):451–460. doi: 10.1002/bies.950150704. [DOI] [PubMed] [Google Scholar]
  25. Hegemann J. H., Pridmore R. D., Schneider R., Philippsen P. Mutations in the right boundary of Saccharomyces cerevisiae centromere 6 lead to nonfunctional or partially functional centromeres. Mol Gen Genet. 1986 Nov;205(2):305–311. doi: 10.1007/BF00430443. [DOI] [PubMed] [Google Scholar]
  26. Hegemann J. H., Shero J. H., Cottarel G., Philippsen P., Hieter P. Mutational analysis of centromere DNA from chromosome VI of Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jun;8(6):2523–2535. doi: 10.1128/mcb.8.6.2523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Jehn B., Niedenthal R., Hegemann J. H. In vivo analysis of the Saccharomyces cerevisiae centromere CDEIII sequence: requirements for mitotic chromosome segregation. Mol Cell Biol. 1991 Oct;11(10):5212–5221. doi: 10.1128/mcb.11.10.5212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Jiang W. D., Philippsen P. Purification of a protein binding to the CDEI subregion of Saccharomyces cerevisiae centromere DNA. Mol Cell Biol. 1989 Dec;9(12):5585–5593. doi: 10.1128/mcb.9.12.5585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kerppola T. K., Curran T. DNA bending by Fos and Jun: the flexible hinge model. Science. 1991 Nov 22;254(5035):1210–1214. doi: 10.1126/science.1957173. [DOI] [PubMed] [Google Scholar]
  30. Kerppola T. K., Curran T. Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell. 1991 Jul 26;66(2):317–326. doi: 10.1016/0092-8674(91)90621-5. [DOI] [PubMed] [Google Scholar]
  31. Kim J., Zwieb C., Wu C., Adhya S. Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene. 1989 Dec 21;85(1):15–23. doi: 10.1016/0378-1119(89)90459-9. [DOI] [PubMed] [Google Scholar]
  32. Kim S., Landy A. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR. Science. 1992 Apr 10;256(5054):198–203. doi: 10.1126/science.1533056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Koudelka G. B. Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins. Nucleic Acids Res. 1991 Aug 11;19(15):4115–4119. doi: 10.1093/nar/19.15.4115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Lechner J., Carbon J. A 240 kd multisubunit protein complex, CBF3, is a major component of the budding yeast centromere. Cell. 1991 Feb 22;64(4):717–725. doi: 10.1016/0092-8674(91)90501-o. [DOI] [PubMed] [Google Scholar]
  35. Masison D. C., Baker R. E. Meiosis in Saccharomyces cerevisiae mutants lacking the centromere-binding protein CP1. Genetics. 1992 May;131(1):43–53. doi: 10.1093/genetics/131.1.43. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. McGrew J., Diehl B., Fitzgerald-Hayes M. Single base-pair mutations in centromere element III cause aberrant chromosome segregation in Saccharomyces cerevisiae. Mol Cell Biol. 1986 Feb;6(2):530–538. doi: 10.1128/mcb.6.2.530. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Mellor J., Jiang W., Funk M., Rathjen J., Barnes C. A., Hinz T., Hegemann J. H., Philippsen P. CPF1, a yeast protein which functions in centromeres and promoters. EMBO J. 1990 Dec;9(12):4017–4026. doi: 10.1002/j.1460-2075.1990.tb07623.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Moitoso de Vargas L., Kim S., Landy A. DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase. Science. 1989 Jun 23;244(4911):1457–1461. doi: 10.1126/science.2544029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Niedenthal R., Stoll R., Hegemann J. H. In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1. Mol Cell Biol. 1991 Jul;11(7):3545–3553. doi: 10.1128/mcb.11.7.3545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Panzeri L., Landonio L., Stotz A., Philippsen P. Role of conserved sequence elements in yeast centromere DNA. EMBO J. 1985 Jul;4(7):1867–1874. doi: 10.1002/j.1460-2075.1985.tb03862.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Robertson C. A., Nash H. A. Bending of the bacteriophage lambda attachment site by Escherichia coli integration host factor. J Biol Chem. 1988 Mar 15;263(8):3554–3557. [PubMed] [Google Scholar]
  42. Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 1991 Aug 30;253(5023):1001–1007. doi: 10.1126/science.1653449. [DOI] [PubMed] [Google Scholar]
  43. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 1988 Oct 25;16(20):9687–9705. doi: 10.1093/nar/16.20.9687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Travers A. A. DNA conformation and protein binding. Annu Rev Biochem. 1989;58:427–452. doi: 10.1146/annurev.bi.58.070189.002235. [DOI] [PubMed] [Google Scholar]
  45. Wechsler D. S., Dang C. V. Opposite orientations of DNA bending by c-Myc and Max. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7635–7639. doi: 10.1073/pnas.89.16.7635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  47. Zinkel S. S., Crothers D. M. DNA bend direction by phase sensitive detection. Nature. 1987 Jul 9;328(6126):178–181. doi: 10.1038/328178a0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES