DNA binding and in vivo function of C. elegans PEB-1 require a conserved FLYWCH motif

Journal of Molecular Biology

Volumn 339, Issue 4, 2004, Pages 695-706

  Beaster Jones, Laura ^a   Okkema, Peter G ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

CD, circular dichroism; DNA binding protein; FLYWCH motif; GFP, green fluorescent protein; NLS, nuclear localization signal; nuclear localization; peb 1; pharynx

Indexed keywords

DNA; HISTIDINE DERIVATIVE; METAL; PHENYLALANYLLEUCYLTYROSYLTRYPTOPHYLCYSTEINYLHISTIDINE; PROTEIN; PROTEIN PEB 1; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; CARBOXY TERMINAL SEQUENCE; CELL NUCLEUS; DNA BINDING; GENETIC CONSERVATION; IN VIVO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF;

CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS;

EID: 2542491134     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.030     Document Type: Article

References (51)

1. Orphanides G., Lagrange T., Reinberg D. The general transcription factors of RNA polymerase II. Genes Dev. 10:1996;2657-2683
2. Blackwood E.M., Kadonaga J.T. Going the distance: a current view of enhancer action. Science. 281:1998;61-63
3. Muller C., Leutz A. Chromatin remodeling in development and differentiation. Curr. Opin. Genet. Dev. 11:2001;167-174
4. Orlando V. Polycomb, epigenomes, and control of cell identity. Cell. 112:2003;599-606
5. de Laat W., Grosveld F. Spatial organization of gene expression: the active chromatin hub. Chromosome Res. 11:2003;447-459
6. Carey M., Smale S.T. Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques. 2000;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
7. Matys V., Fricke E., Geffers R., Gossling E., Haubrock M., Hehl R., et al. TRANSFAC:. transcriptional regulation, from patterns to profiles. Nucl. Acids Res. 31:2003;374-378
8. Thatcher J.D., Fernandez A.P., Beaster-Jones L., Haun C., Okkema P.G. The Caenorhabditis elegans peb-1 gene encodes a novel DNA-binding protein involved in morphogenesis of the pharynx, vulva, and hindgut. Dev. Biol. 229:2001;480-493
9. Okkema P.G., Fire A. The Caenorhabditis elegans NK-2 class homeoprotein CEH-22 is involved in combinatorial activation of gene expression in pharyngeal muscle. Development. 120:1994;2175-2186
10. Kalb J.M., Beaster-Jones L., Fernandez A.P., Okkema P.G., Goszczynski B., McGhee J.D. Interference between the PHA-4 and PEB-1 transcription factors in formation of the Caenorhabditis elegans pharynx. J. Mol. Biol. 320:2002;697-704
11. Dorn R., Krauss V. The modifier of mdg4 locus in Drosophila: functional complexity is resolved by trans splicing. Genetica. 117:2003;165-177
12. Buchner K., Roth P., Schotta G., Krauss V., Saumweber H., Reuter G., Dorn R. Genetic and molecular complexity of the position effect variegation modifier mod(mdg4) in Drosophila. Genetics. 155:2000;141-157
13. Gerasimova T.I., Gdula D.A., Gerasimov D.V., Simonova O., Corces V.G. A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell. 82:1995;587-597
14. Georgiev P., Kozycina M. Interaction between mutations in the suppressor of Hairy wing and modifier of mdg4 genes of Drosophila melanogaster affecting the phenotype of gypsy-induced mutations. Genetics. 142:1996;425-436
15. Dorn R., Krauss V., Reuter G., Saumweber H. The enhancer of position-effect variegation of Drosophila, E(var)3-93D, codes for a chromatin protein containing a conserved domain common to several transcriptional regulators. Proc. Natl Acad. Sci. USA. 90:1993;11376-11380
16. Chen S., Corces V.G. The gypsy insulator of Drosophila affects chromatin structure in a directional manner. Genetics. 159:2001;1649-1658
17. Cai H., Levine M. Modulation of enhancer-promoter interactions by insulators in the Drosophila embryo. Nature. 376:1995;533-536
18. Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N., et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1:2003;E45
19. Rechsteiner M., Rogers S.W. PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 21:1996;267-271
20. Coleman J.E. Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins. Annu. Rev. Biochem. 61:1992;897-946
21. Pollock R.M. Determination of protein-DNA sequence specificity by PCR-assisted binding-site selection. Ausubel F.M. Current Protocols in Molecular Biology. 1996;Wiley, New York
22. Lee S., Garfinkel M.D. Characterization of Drosophila OVO protein DNA binding specificity using random DNA oligomer selection suggests zinc finger degeneration. Nucl. Acids Res. 28:2000;826-834
23. Patthy L. Protein Evolution. 1999;Blackwell Science, Oxford
24. Johnson P.F., McKnight S.L. Eukaryotic transcriptional regulatory proteins. Annu. Rev. Biochem. 58:1989;799-839
25. Margolin J.F., Friedman J.R., Meyer W.K., Vissing H., Thiesen H.J., Rauscher F.J. 3rd. Kruppel-associated boxes are potent transcriptional repression domains. Proc. Natl Acad. Sci. USA. 91:1994;4509-4513
26. Triezenberg S.J. Structure and function of transcriptional activation domains. Curr. Opin. Genet. Dev. 5:1995;190-196
27. Krause M., Harrison S.W., Xu S.Q., Chen L., Fire A. Elements regulating cell- and stage-specific expression of the C. elegans MyoD family homolog hlh-1. Dev. Biol. 166:1994;133-148
28. Harfe B.D., Fire A. Muscle and nerve-specific regulation of a novel NK-2 class homeodomain factor in Caenorhabditis elegans. Development. 125:1998;421-429
29. Gilleard J.S., Shafi Y., Barry J.D., McGhee J.D. ELT-3: a Caenorhabditis elegans GATA factor expressed in the embryonic epidermis during morphogenesis. Dev. Biol. 208:1999;265-280
30. Burglin T.R., Aspock G. Exon duplication from a fork head to a homeodomain protein. Dev. Genes Evol. 209:1999;629-633
31. Molin L., Mounsey A., Aslam S., Bauer P., Young J., James M., Sharma-Oates A., et al. Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues. Development. 127:2000;4825-4835
32. Parkinson J., Whitton C., Guiliano D., Daub J., Blaxter M. 200, 000 nematode expressed sequence tags on the Net. Trends Parasitol. 17:2001;394-396
33. Rubin G.M., Yandell M.D., Wortman J.R., Gabor Miklos G.L., Nelson C.R., Hariharan I.K., et al. Comparative genomics of the eukaryotes. Science. 287:2000;2204-2215
34. Ruvkun G., Hobert O. The taxonomy of developmental control in Caenorhabditis elegans. Science. 282:1998;2033-2041
35. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., et al. The Pfam protein families database. Nucl. Acids Res. 30:2002;276-280
36. Ghosh D., Gerasimova T.I., Corces V.G. Interactions between the Su(Hw) and Mod(mdg4) proteins required for gypsy insulator function. EMBO J. 20:2001;2518-2527
37. Gerasimova T.I., Corces V.G. Polycomb and trithorax group proteins mediate the function of a chromatin insulator. Cell. 92:1998;511-521
38. Andrulis E.D., Zappulla D.C., Ansari A., Perrod S., Laiosa C.V., Gartenberg M.R., Sternglanz R. Esc1, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Mol. Cell. Biol. 22:2002;8292-8301
39. Walhout A.J., Sordella R., Lu X., Hartley J.L., Temple G.F., Brasch M.A., et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science. 287:2000;116-122
40. Steadman D.J., Giuffrida D., Gelmann E.P. DNA-binding sequence of the human prostate-specific homeodomain protein NKX3.1. Nucl. Acids Res. 28:2000;2389-2395
41. Nomura M., Takihara Y., Abdul Motaleb M., Horie K., Higashinakagawa T., Shimada K. Sequence-specific DNA binding activity in the RAE28 protein, a mouse homologue of the Drosophila polyhomeotic protein. Biochem. Mol. Biol. Int. 46:1998;905-912
42. Shirai M., Osugi T., Koga H., Kaji Y., Takimoto E., Komuro I., et al. The Polycomb-group gene Rae28 sustains Nkx2.5/Csx expression and is essential for cardiac morphogenesis. J. Clin. Invest. 110:2002;177-184
43. Gaudet J., Mango S.E. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science. 295:2002;821-825
44. Lewis J.A., Fleming J.T. Basic culture methods. Biology M.i C. Caenorhabditis elegans: Modern Biological Analysis of an Organism. Vol. 48:1995;4-30 Academic Press, San Diego, CA
45. Mello C., Fire A. DNA transformation. Epstein H.F., Shakes D.C. Caenorhabditis elegans: Modern Biological Analysis of an Organism. Vol. 48:1995;451-482 Academic Press, San Diego, CA
46. Ausubel F.M. Current Protocols in Molecular Biology. 1990;Greene Pub. Associates and Wiley-Interscience, New York
47. Krause M. Techniques for analyzing transcription and translation. Epstein H., Shakes D.C. Caenorhabditis elegans: Modern Biological Analysis of an Organism. Vol. 48:1995;513-533 Academic Press, San Diego, CA
48. Thatcher J.D., Haun C., Okkema P.G. The DAF-3 Smad binds DNA and represses gene expression in the Caenorhabditis elegans pharynx. Development. 126:1999;97-107
49. Bellini M., Lacroix J.C., Gall J.G. A zinc-binding domain is required for targeting the maternal nuclear protein PwA33 to lampbrush chromosome loops. J. Cell Biol. 131:1995;563-570
50. Pfister T., Jones K.W., Wimmer E. A cysteine-rich motif in poliovirus protein 2C(ATPase) is involved in RNA replication and binds zinc in vitro. J. Virol. 74:2000;334-343
51. Kalb J.M., Lau K.K., Goszczynski B., Fukushige T., Moons D., Okkema P.G., McGhee J.D. pha-4 is Ce-fkh-1, a fork head/HNF-3alpha, beta, gamma homolog that functions in organogenesis of the C. elegans pharynx. Development. 125:1998;2171-2180