Regulation of Trypanosome DNA Glycosylation by a SWI2/SNF2-like Protein

Molecular Cell

Volumn 17, Issue 3, 2005, Pages 441-451

  Dipaolo, Courtney ^a   Kieft, Rudo ^a   Cross, Mike ^b   Sabatini, Robert ^a  

^a MARINE BIOLOGICAL LABORATORY   (United States)

^b NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; J BINDING PROTEIN 2; PROTOZOAL DNA; UNCLASSIFIED DRUG;

ARTICLE; CHROMOSOME; DNA GLYCOSYLATION; GLYCOSYLATION; INDUCED MUTATION; MOLECULAR MODEL; NONHUMAN; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN SYNTHESIS; TRYPANOSOMA; UPREGULATION;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CELL LINE; CELL NUCLEUS; DNA, PROTOZOAN; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, PROTOZOAN; GLUCOSIDES; GLYCOSYLATION; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; TRANSFECTION; TRYPANOSOMA BRUCEI BRUCEI; URACIL;

TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 13244251108     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.12.022     Document Type: Article

References (41)

1. Biebinger S., Wirtz L.E., Clayton C. Vectors for inducible over-expression of potentially toxic gene products in bloodstream and procyclic Trypanosoma brucei. Mol. Biochem. Parasitol. 85:1997;99-112
2. Blundell P.A., van Leeuwen F., Brun R., Borst P. Changes in expression site control and DNA modification in Trypanosoma brucei during differentiation of the bloodstream form to the procyclic form. Mol. Biochem. Parasitol. 93:1998;115-130
3. Borst P., van Leeuwen F. beta-D-glucosyl-hydroxymethyluracil, a novel base in African trypanosomes and other Kinetoplastida. Mol. Biochem. Parasitol. 90:1997;1-8
4. Borst P., Gommers-Ampt J.H., Ligtenberg M.J., Rudenko G., Kieft R., Taylor M.C., Blundell P.A., van Leeuwen F. Control of antigenic variation in African trypanosomes. Cold Spring Harb. Symp. Quant. Biol. 58:1993;105-114
5. Brzeski J., Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278:2003;823-828
6. Carruthers V.B., van der Ploeg L.H., Cross G.A. DNA-mediated transformation of bloodstream-form Trypanosoma brucei. Nucleic Acids Res. 21:1993;2537-2538
7. Cross M., Kieft R., Sabatini R., Wilm M., de Kort M., van der Marel G., van Boom J., van Leeuwen F., Borst P. The modified base J is the target for a novel DNA-binding protein in kinetoplastid protozoans. EMBO J. 18:1999;6573-6581
8. Cross M., Kieft R., Sabatini R., Dirks-Mulder A., Chaves I., Borst P. J binding protein increases the level and retention of the unusual base J in trypanosome DNA. Mol. Microbiol. 46:2002;37-47
9. Dennis K., Fan T., Geiman T., Yan Q., Muegge K. Lsh, a member of the SNF2 family is required for genome-wide methylation. Genes Dev. 15:2001;2940-2944
10. Deuring R., Fanti L., Armstrong J.A., Sarte M., Papoulas O., Prestel M., Daubresse G., Verardo M., Moseley S.L., Berloco M., et al. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Mol. Cell. 5:2000;355-365
11. Eisen J.A., Sweder K.S., Hanawalt P.C. Evolution of the SNF2 family of proteins. subfamilies with distinct sequences and functions Nucleic Acids Res. 23:1995;2715-2723
12. Fazzio T.G., Kooperberg C., Goldmark J.P., Neal C., Basom R., Delrow J., Tsukiyama T. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21:2001;6450-6460
13. Flaus A., Owen-Hughes T. Mechanisms for ATP-dependent chromatin remodelling. Curr. Opin. Genet. Dev. 11:2001;148-154
14. Gibbons R.J., McDowell T.L., Raman S., O'Rourke D.M., Garric D., Ayyub H., Higgs D.R. Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation. Nat. Genet. 24:2000;368-371
15. Gommers-Ampt J.H., Van Leeuwen F., de Beer A.L., Vliegenthart J.F., Dizdaroglu M., Kowalak J.A., Crain P.F., Borst P. Beta-D-glucosyl- hydroxymethyluracil. a novel modified base present in the DNA of the parasitic protozoan T. brucei Cell. 75:1993;1129-1136
16. Gorbalenya A.E., Koonin E.V., Donchenko A.P., Blinov V.M. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17:1989;4713-4730
17. Hirumi H., Hirumi K., Doyle J.J., Cross G.A. In vitro cloning of animal-infective bloodstream forms of Trypanosoma brucei. Parasitology. 80:1980;371-382
18. Jeddeloh J.A., Stokes T.L., Richards E.J. Maintenance of genominc methylation requires a SWI/SNF-like protein. Nat. Genet. 22:1999;94-97
19. Jones P.L., Veenstra G.J., Wade P.A., Vermaak D., Kass S.U., Landsberger N., Strouboulis J., Wolffe A.P. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19:1998;187-191
20. Kakutani T., Jeddeloh J.A., Richards E.J. Characterization of an Arabidopsis thaliana DNA hypomethylation mutant. Nucleic Acids Res. 23:1995;130-137
21. Langst G., Becker P.B. Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J. Cell Sci. 114:2001;2561-2568
22. Marchetti M.A., Tschudi C., Kwon H., Wolin S.L., Ullu E. Import of proteins into the trypanosome nucleus and their distribution at karyokinesis. J. Cell Sci. 113:2000;899-906
23. Muchardt C., Yaniv M. ATP-dependent chromatin remodelling. SWI/SNF and Co. are on the job J. Mol. Biol. 293:1999;187-198
24. Pollard V.W., Sabatini R., Hajduk S.L. Molecular and Biochemical Methods for Analysis of Kinetoplastid RNA Editing. Adolf K.W. Methods in Molecular Genetics, Volume III. 1994;61-87 Academic Press, New York
25. Richmond E., Peterson C.L. Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2. Nucleic Acids Res. 24:1996;3685-3692
26. Rudenko G., Blundell P.A., Taylor M.C., Kieft R., Borst P. VSG gene expression site control in insect form Trypanosoma brucei. EMBO J. 13:1994;5470-5482
27. Rudenko G., Blundell P.A., Dirks-Mulder A., Kieft R., Borst P. A ribosomal DNA promoter replacing the promoter of a telomeric VSG gene expression site can be efficiently switched on and off in T. brucei. Cell. 83:1995;547-553
28. Rudenko G., McCulloch R., Dirks-Mulder A., Borst P. Telomere exchange can be an important mechanism of variant surface glycoprotein gene switching in Trypanosoma brucei. Mol. Biochem. Parasitol. 80:1996;60-75
29. Sabatini R., Meeuwenoord N., van Boom J.H., Borst P. Recognition of base J in duplex DNA by J-binding protein. J. Biol. Chem. 277:2002;958-966. a
30. Sabatini R., Meeuwenoord N., van Boom J.H., Borst P. Site-specific interactions of JBP with base and sugar moieties in duplex J-DNA. J. Biol. Chem. 277:2002;28150-28156. b
31. Sudarsanam P., Iyer V., Brown P.O., Winston F. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 97:2000;3364-3369
32. Tschudi C., Young A.S., Ruben L., Patton C.L., Richards F.F. Calmodulin genes in Trypanosomes are tandemly repeated and produce multiple mRNAs with a common 5′ leader sequence. Proc. Natl. Acad. Sci. USA. 82:1985;3998-4002
33. Ulbert S., Cross M., Boorstein R., Teebor G.W., Borst P. Expression of the human DNA glycosylase hSMUG1 in Trypanosoma brucei causes DNA damage and interferes with J biosynthesis. Nucleic Acids Res. 30:2002;3919-3926
34. van den Hoff M.J., Moorman A.F., Lamers W.H. Electroporation in 'intracellular' buffer increases cell survival. Nucleic Acids Res. 20:1992;2902
35. van Leeuwen F., Wijsman E.R., Kuyl-Yeheskiely E., van der Marel G.A., van Boom J.H., Borst P. The telomeric GGGTTA repeats of Trypanosoma brucei contain the hypermodified base J in both strands. Nucleic Acids Res. 24:1996;2476-2482
36. van Leeuwen F., Wijsman E.R., Kieft R., van der Marel G.A., van Boom J.H., Borst P. Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. Genes Dev. 11:1997;3232-3241
37. van Leeuwen F., Kieft R., Cross M., Borst P. Biosynthesis and function of the modified DNA base beta-D-glucosyl-hydroxymethyluracil in Trypanosoma brucei. Mol. Cell. Biol. 18:1998;5643-5651. a
38. van Leeuwen F., Taylor M.C., Mondragon A., Moreau H., Gibson W., Kieft R., Borst P. beta-D-glucosyl-hydroxymethyluracil is a conserved DNA modification in kinetoplastid protozoans and is abundant in their telomeres. Proc. Natl. Acad. Sci. USA. 95:1998;2366-2371. b
39. van Leeuwen F., Kieft R., Cross M., Borst P. Tandemly repeated DNA is a target for the partial replacement of thymine by beta-D-glucosal- hydroxymethyluracil in Trypanosoma brucei. Mol. Biochem. Parasitol. 109:2000;133-145
40. Wirtz E., Leal S., Ochatt C., Cross G.A. A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei. Mol. Biochem. Parasitol. 99:1999;89-101
41. Yoo E.J., Jin Y.H., Jang Y.K., Bjerling P., Tabish M., Hong S.H., Ekwall K., Park S.D. Fission yeast hrp1, a chromodomain ATPase, is required for proper chromosome segregation and its overexpression interferes with chromatin condensation. Nucleic Acids Res. 28:2000;2004-2011