Gene regulation in planta by plant-derived engineered zinc finger protein transcription factors

Plant Molecular Biology

Volumn 57, Issue 3, 2005, Pages 411-423

  Holmes Davis, Rachel ^a   Li, Guofu ^b   Jamieson, Andrew C ^e   Rebar, Edward J ^e   Liu, Qiang ^c   Kong, Yanhong ^e   Case, Casey C ^e   Gregory, Philip D ^d  

^a PLANT GENE EXPRESSION CENTER   (United States)

^b Agronomic Traits Department   (United States)

^c Avidia Research Institute   (United States)

^d SANGAMO BIOSCIENCES INC   (United States)

^e NONE

Author keywords

Alcohol dehydrogenase; Arabidopsis; Gene regulation; Protein engineering; Transcriptional regulation; Transgenic plants; Zinc finger proteins; Zinc motifs

Indexed keywords

AGRICULTURE; BIOTECHNOLOGY; DNA SEQUENCES; GENES; GENETIC ENGINEERING; PROTEINS; ZINC;

DNA-PROTEIN INTERACTION; GENE REGULATION; TRANSCRIPTION FACTORS (TF); ZINC FINGER PROTEINS (ZFP);

PLANTS (BOTANY);

ALCOHOL DEHYDROGENASE; DNA BINDING PROTEIN; HYBRID PROTEIN; MESSENGER RNA; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN; ZINC FINGER PROTEIN;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BINDING COMPETITION; BINDING SITE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; PLANT LEAF; SEQUENCE HOMOLOGY; TRANSGENIC PLANT; UPREGULATION;

ALCOHOL DEHYDROGENASE; AMINO ACID SEQUENCE; ARABIDOPSIS; BINDING SITES; BINDING, COMPETITIVE; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE DATA; PLANT LEAVES; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; RECOMBINANT FUSION PROTEINS; RNA, MESSENGER; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; UP-REGULATION; ZINC FINGERS;

AGRICULTURE; BIOTECHNOLOGY; GENES; GENETIC ENGINEERING; NUCLEIC ACIDS; PLANTS; PROTEINS; ZINC;

ARABIDOPSIS; MAMMALIA;

EID: 17744384583     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-004-7820-x     Document Type: Article

References (54)

1. V.V. Bartsevich R.L. Juliano 2000 Regulation of the MDR1 gene by transcriptional repressors selected using peptide combinatorial libraries Mol. Pharmacol. 58 1 10
2. R.R. Beerli B. Dreier C.F. Barbas 3rd 2000a Positive and negative regulation of endogenous genes by designed transcription factors Proc. Natl. Acad. Sci. USA 97 1495 500
3. R.R. Beerli U. Schopfer B. Dreier C.F. Barbas 3rd 2000b Chemically regulated zinc finger transcription factors J. Biol. Chem. 275 32617 32627
4. R.R. Beerli D.J. Segal B. Dreier C.F. Barbas 3rd 1998 Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks Proc. Natl. Acad. Sci. USA 95 14628 14633
5. P. Bilodeau M. Luo E.S. Dennis J. Peacock A.M. Chaudhury 1998 Cloning of a cDNA encoding a two fingered C2H2 zinc finger protein Plant. Phys. 116 1193
6. S.J. Clough A.F. Bent 1998 Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana Plant J. 16 735 743
7. J.R. Desjarlais J.M. Berg 1992 Toward rules relating zinc finger protein sequences and DNA binding site preferences Proc. Natl. Acad. Sci. USA 89 7345 7349
8. J.M. Dunwell 2000 Transgenic approaches to crop improvement J. Exp. Bot. 51 487 496
9. M. Elrod-Erickson T.E. Benson C.O. Pabo 1998 High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition Structure 6 451 464
10. B.J. Feys L.J. Moisan M.A. Newman J.E. Parker 2001 Direct interaction between the Arabidopsis disease resistance signaling proteins, EDS1 and PAD4 Embo J 20 5400 5411
11. G.N. Filippova S. Fagerlie E.M. Klenova C. Myers Y. Dehner G. Goodwin P.E. Neiman S.J. Collins V.V. Lobanenkov 1996 An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes Mol. Cell. Biol. 16 2802 2813
12. J Finnegan D. McElroy 1994 Transgene inactivation: plants fight back! Biotechnology 12 883 888
13. S.A. Goff K.C. Cone M.E. Fromm 1991 Identification of functional domains in the maize transcriptional activator C1: comparison of wild-type and dominant inhibitor proteins Genes Dev. 5 298 309
14. A. Green B. Sarkar 1998 Alteration of zif268 zinc finger motifs gives rise to non-native zinc- co-ordination sites but preserves wild-type DNA recognition Biochem. J. 333 85 90
15. H.A. Greisman C.O. Pabo 1997 A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites Science 275 657 661
16. D.S. Gross W.T. Garrard 1998 Nuclease hypersensitive sites in chromatin Annu. Rev. Biochem. 57 159 197
17. X. Guan J. Stege M. Kim Z. Dahmani N. Fan P. Heifetz C.F. Barbas 3rd S.P. Briggs 2002 Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors Proc. Natl. Acad. Sci. USA 99 13296 301
18. Y. Hori K. Susuki Y. Okuno M. Nagaoka S. Futaki Y. Sugiura 2000 Atificial zinc finger peptide containing a novel His4 domain J. Am. Chem. Soc. 122 7648 7653
19. C. Isernia E. Bucci M. Leone L. Zaccaro P. Di Lello G. Digilio S. Esposito M. Saviano B. Di Blasio C. Pedone P.V. Pedone R. Fattorusso 2003 NMR structure of the single QALGGH Zinc finger domain from the Arabidopsis thaliana SUPERMAN Protein Chembiochem 4 171 80
20. BA Krizek D.L. Merkle J.M. Berg 1993 Ligand variation and metal ion binding specificity in zinc finger peptides Inorg. Chem. 32 937 940
21. K. Kubo A. Sakamoto A. Kobayashi Z. Rybka Y. Kanno H. Nakagawa H. Takatsuji 1998 Cys2/His2 zinc finger protein family of petunia: evolution and general mechanism of target-sequence recognition Nucleic Acids Res. 26 608 615
22. S.P. Kumpatla M.B. Chandrasekhara L.M. Iyer G. Li T.C. Hall 1998 Genome intruder scanning and modulation systems and transgene silencing Trends Plant Sci. 3 97 104
23. E.S. Lander L.M. Linton B. Birren C. Nusbaum M.C. Zody J. Baldwin K. Devon K. Dewar M. Doyle W. FitzHugh R. Funke D. Gage K. Harris A. Heaford J. Howland L. Kann J. Lehoczky R. LeVine P. McEwan K. McKernan J. Meldrim J.P. Mesirov C. Miranda W. Morris J. Naylor C. Raymond M. Rosetti R. Santos A. Sheridan C Sougnez N. Stange-Thomann N. Stojanovic A. Subramanian D. Wyman J. Rogers J. Sulston R. Ainscough S. Beck D. Bentley J. Burton C. Clee N. Carter A. Coulson R. Deadman P. Deloukas A. Dunham I. Dunham R. Durbin L. French D. Grafham S. Gregory T. Hubbard S. Humphray A. Hunt M. Jones C. Lloyd A. McMurray L. Matthews S. Mercer S. Milne J.C. Mullikin A. Mungall R. Plumb M. Ross R. Shownkeen S. Sims R.H. Waterston R.K. Wilson L.W. Hillier J.D. McPherson M.A. Marra E.R. Mardis L.A. Fulton A.T. Chinwalla K.H. Pepin W.R. Gish S.L. Chissoe M.C. Wendl K.D. Delehaunty T.L. Miner A. Delehaunty J.B. Kramer L.L. Cook R.S. Fulton D.L. Johnson P.J. Minx S.W. Clifton T. Hawkins E. Branscomb P. Predki P. Richardson S. Wenning T Slezak N. Doggett J.F. Cheng A. Olsen S. Lucas C. Elkin E. Uberbacher M. Frazier 2001 Initial sequencing and analysis of the human genome Nature 409 860 921
24. M.L. Lesnick V.L. Chandler 1998 Activation of the maize anthocyanin gene a2 is mediated by an element conserved in many anthocyanin promoters Plant Physiol. 117 437 445
25. G. Li S.P. Chandler A.P. Wolffe T.C. Hall 1998 Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation Proc. Natl. Acad. Sci. USA 95 4772 4777
26. P.Q. Liu E.J. Rebar L. Zhang Q. Liu A.C. Jamieson Y. Liang H. Qi P.X. Li B. Chen M.C. Mendel X. Zhong Y.L. Lee S.P. Eisenberg S.K. Spratt C.C. Case A.P. Wolffe 2001 Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A J. Biol. Chem. 276 11323 11334
27. Q. Liu Z. Xia X. Zhong C.C. Case 2002 Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol Chem. 277 3850 3856
28. L. Miele 1997 Plants as bioreactors for biopharmaceuticals: regulatory considerations Trends Biotechnol. 15 45 50
29. M.I. Ordiz C.F. Barbas 3rd R.N. Beachy 2002 Regulation of transgene expression in plants with polydactyl zinc finger transcription factors Proc. Natl. Acad. Sci. USA 99 13290 13295
30. C.O. Pabo L. Nekludova 2000 Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol. 301 597 624
31. C.O. Pabo E. Peisach R.A. Grant 2001 Design and selection of novel Cys2His2 zinc finger proteins Annu Rev Biochem 70 313 340
32. E.J. Rebar Y. Huang R. Hickey A.K. Nath D. Meoli S. Nath B. Chen L. Xu Y. Liang A.C. Jamieson L. Zhang S.K. Spratt C.C. Case A. Wolffe F.J. Giordano 2002 Induction of angiogenesis in a mouse model using engineered transcription factors Nat Med 8 1427 1432
33. J.L. Riechmann J. Heard G. Martin L. Reuber C. Jiang J. Keddie L. Adam O. Pineda O.J. Ratcliffe R.R. Samaha R. Creelman M. Pilgrim P. Broun J.Z. Zhang D. Ghandehari B.K. Sherman G. Yu 2000 Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes Science 290 2105 2110
34. R.J. Rooney K. Rothammer E.R. Fernandes 1998 Mutational analysis of p50E4F suggests that DNA binding activity is mediated through an alternative structure in a zinc finger domain that is regulated by phosphorylation Nucleic Acids Res. 26 1681 168
35. H. Sakamoto T. Araki T. Meshi M. Iwabuchi 2000 Expression of a subset of the Arabidopsis Cys(2)/His(2)-type zinc- finger protein gene family under water stress Gene 248 23 32
36. J.P. Sanchez C. Ullman M. Moore Y. Choo N.H. Chua 2002 Regulation of Gene Expression in Arabidopsis thaliana by artificial Zinc finger chimeras Plant Cell Physiol. 43 1465 1472
37. R. Schuh W. Aicher U. Gaul S. Cote A. Preiss D. Maier E. Seifert U. Nauber C. Schroder R. Kemler 1986 A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Kruppel, a Drosophila segmentation gene Cell 47 1025 1032
38. D.J. Segal J.T. Stege C.F. Barbas 3rd 2003 Zinc fingers and a green thumb: manipulating gene expression in plants Curr. Opin. Plant Biol. 6 163 168
39. R.E. Sheehy M. Kramer W.R. Hiatt 1998 Reduction of polygalacturonase activity in tomato fruit by antisense RNA Proc. Natl. Acad. Sci. USA 85 8805 8809
40. Y. Shi J.M. Berg 1995 A direct comparison of the properties of natural and designed zinc finger proteins Chem. Biol. 2 83 89
41. C.J.S. Smith C.F. Watson J. Ray C.R. Bird P.C. Morris W. Schuch D. Grierson 1998 Antisense RNA inhibition of polygalacturonase gne expression in transgenic tomatoes Nature 334 724 726
42. J.T. Stege X. Guan T. Ho R.N. Beachy C.F. Barbas 3rd 2002 Controlling gene expression in plants using synthetic zinc finger transcription factors Plant J. 32 1077 1086
43. B.W. Tague H.M. Goodman 1995 Characterization of a family of Arabidopsis zinc finger protein cDNAs Plant Mol. Biol. 28 267 279
44. H. Takatsuji 1998 Zinc-finger transcription factors in plants Cell Mol. Life Sci. 54 582 596
45. S. Tan D. Guschin A. Davalos Y.L. Lee A.W. Snowden Y. Jouvenot H.S. Zhang K. Howes A.R. McNamara A. Lai C. Ullman L. Reynolds M. Moore M. Isalan L.P. Berg B. Campos H. Qi S.K. Spratt C.C. Case C.O. Pabo J. Campisi P.D. Gregory 2003 Zinc-finger protein-targeted gene regulation: genomewide single-gene specificity Proc. Natl. Acad. Sci. USA 100 11997 2002
46. B. Toth 2000 A review of the natural occurrence, synthetic production and use of carcinogenic hydrazines and related chemicals In vivo 14 299 319
47. R. Tupler G. Perini M.R. Green 2001 Expressing the human genome Nature 409 832 833
48. C.A. Turner Jr. D.H. Mack M.M. Davis 1994 Blimp-1, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin-secreting cells Cell 77 297 306
49. A.L. Van Eenennaam G. Li M. Venkatramesh C. Levering X. Gong A.C. Jamieson E.J. Rebar C.K. Shewmaker C.C. Case 2004 Elevation of seed alpha-tocopherol levels using plant-based transcription factors targeted to an endogenous locus Metab. Eng. 6 101 108
50. M.J. Varagona R.J. Schmidt N.V. Raikhel 1992 Nuclear localization signal(s) required for nuclear targeting of the maize regulatory protein Opaque-2 Plant Cell 4 1213 1227
51. S.A. Wolfe R.A. Grant M. Elrod-Erickson C.O. Pabo 2001 Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes Structure (Camb) 9 717 723
52. S.A. Wolfe L. Nekludova C.O. Pabo 2000 DNA recognition by Cys2His2 zinc finger proteins Annu. Rev. Biophys. Biomol. Struct. 29 183 212
53. C. Xiang P. Han I. Lutziger K. Wang D.J. Oliver 1999 A mini binary vector series for plant transformation Plant Mol. Biol. 40 711 717
54. L. Zhang S.K. Spratt Q. Liu B. Johnstone H. Qi E.E. Raschke A.C. Jamieson E.J. Rebar A.P. Wolffe C.C. Case 2000 Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene J. Biol. Chem. 275 33850 33860