Competitive inhibition of transcription factors by small interfering peptides

Trends in Plant Science

Volumn 16, Issue 10, 2011, Pages 541-549

  Seo, Pil Joon ^a   Hong, Shin Young ^a   Kim, Sang Gyu ^b   Park, Chung Mo ^a,c  

^a Seoul National University   (South Korea)

^b MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

^c Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; PEPTIDE; TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; ARABIDOPSIS; BINDING COMPETITION; BIOLOGICAL MODEL; BIOTECHNOLOGY; CHEMISTRY; DRUG ANTAGONISM; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; REVIEW;

ALTERNATIVE SPLICING; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BINDING, COMPETITIVE; BIOTECHNOLOGY; GENE EXPRESSION REGULATION, PLANT; MODELS, GENETIC; PEPTIDES; TRANSCRIPTION FACTORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 80053333872     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2011.06.001     Document Type: Review

References (91)

1. Behm-Ansmant I., et al. MicroRNAs silence gene expression by repressing protein expression and/or by promoting mRNA decay. Cold Spring Harb. Symp. Quant. Biol. 2006, 71:523-530.
2. Yun J., et al. Small interfering peptides as a novel way of transcriptional control. Plant Signal. Behav. 2008, 3:615-617.
3. Spoel S.H., et al. Post-translational protein modification as a tool for transcription reprogramming. New Phytol. 2010, 186:333-339.
4. Hammell C.M. The microRNA-argonaute complex: a platform for mRNA modulation. RNA Biol. 2008, 5:123-127.
5. Chuck G., et al. Big impacts by small RNAs in plant development. Curr. Opin. Plant Biol. 2008, 12:81-86.
6. Seo P.J., et al. Membrane-bound transcription factors in plants. Trends Plant Sci. 2008, 13:550-556.
7. Seo P.J., et al. Cold activation of a plasma membrane-tethered NAC transcription factor induces a pathogen resistance response in Arabidopsis. Plant J. 2010, 61:661-671.
8. Seo P.J., et al. Proteolytic processing of an Arabidopsis membrane-bound NAC transcription factor is triggered by cold-induced changes in membrane fluidity. Biochem. J. 2010, 427:359-367.
9. Roudier F., et al. Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet. 2009, 25:511-517.
10. Feng S., et al. Epigenetic reprogramming in plant and animal development. Science 2010, 330:622-627.
11. Sáez-Vásquez J., Gadal O. Genome organization and function: a view from yeast and Arabidopsis. Mol. Plant 2010, 3:678-690.
12. Kwon C.S., Wagner D. Unwinding chromatin for development and growth: a few genes at a time. Trends Genet. 2007, 23:403-412.
13. Kosugi S., Ohashi Y. DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 2002, 30:337-348.
14. van der Graaff E., et al. The WUS homeobox-containing (WOX) protein family. Genome Biol. 2009, 10:248.
15. Izawa T., et al. Plant bZIP protein DNA binding specificity. J. Mol. Biol. 1993, 230:1131-1144.
16. Vinson C., et al. Deciphering B-ZIP transcription factor interactions in vitro and in vivo. Biochim. Biophys. Acta 2006, 1759:4-12.
17. Amoutzias G.D., et al. Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem. Sci. 2008, 33:220-229.
18. Wenkel S., et al. A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes. Plant Cell 2007, 19:3379-3390.
19. Kim Y.S., et al. HD-ZIP III activity is modulated by competitive inhibitors via a feedback loop in Arabidopsis shoot apical meristem development. Plant Cell 2008, 20:920-933.
20. Fukaki H., et al. Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14 alters lateral root development in Arabidopsis. Plant J. 2005, 44:382-395.
21. Weijers D., et al. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO J. 2005, 24:1874-1885.
22. Szemenyei H., et al. TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science 2008, 319:1384-1386.
23. Ploense S.E., et al. A gain-of-function mutation in IAA18 alters Arabidopsis embryonic apical patterning. Development 2009, 136:1509-1517.
24. Liscum E., Reed J.W. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol. Biol. 2002, 49:387-400.
25. Benezra R., et al. The protein Id: a negative regulator of helix-loop-helix DNA binding proteins. Cell 1990, 61:49-59.
26. Hu W., Ma H. Characterization of a novel putative zinc finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development. Plant J. 2006, 45:399-422.
27. Hong S.Y., et al. Nuclear import and DNA binding of the ZHD5 transcription factor is modulated by a competitive peptide inhibitor in Arabidopsis. J. Biol. Chem. 2011, 286:1659-1668.
28. Seo P.J., et al. Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism. Nat. Commun. 2011, 2:303.
29. Maitra U., et al. Differentiation-induced cleavage of Cutl1/CDP generates a novel dominant-negative isoform that regulates mammary gene expression. Mol. Cell Biol. 2006, 26:7466-7478.
30. Chang J., et al. Inhibitory cardiac transcription factor, SRF-N, is generated by caspase 3 cleavage in human heart failure and attenuated by ventricular unloading. Circulation 2003, 108:407-413.
31. Privé G.G., Melnick A. Specific peptides for the therapeutic targeting of oncogenes. Curr. Opin. Genet. Dev. 2006, 16:71-77.
32. Polo J.M., et al. Specific peptide interference reveals BCL6 transcriptional and oncogenic mechanisms in B-cell lymphoma cells. Nat. Med. 2004, 10:1329-1335.
33. Staudt A.C., Wenkel S. Regulation of protein function by microProteins. EMBO Rep. 2011, 12:35-42.
34. Berleth T., et al. Auxin signals-turning genes on and turning cells around. Curr. Opin. Plant Biol. 2004, 7:553-563.
35. Tiwari S.B., et al. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell 2004, 16:533-543.
36. Hagen G., Guilfoyle T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol. Biol. 2002, 49:373-385.
37. Reed J.W. Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci. 2001, 6:420-425.
38. Fukaki H., et al. PICKLE is required for SOLITARY-ROOT/IAA14-mediated repression of ARF7 and ARF19 activity during Arabidopsis lateral root initiation. Plant J. 2006, 48:380-389.
39. Hardtke C.S., et al. Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4. Development 2004, 131:1089-1100.
40. Chico J.M., et al. JAZ repressors set the rhythm in jasmonate signaling. Curr. Opin. Plant Biol. 2008, 11:486-494.
41. Davière J.M., et al. Transcriptional factor interaction: a central step in DELLA function. Curr. Opin. Genet. Dev. 2008, 18:295-303.
42. Feng S., et al. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 2008, 451:475-479.
43. de Lucas M., et al. A molecular framework for light and gibberellin control of cell elongation. Nature 2008, 451:480-484.
44. Elhiti M., Stasolla C. Structure and function of homeodomain-leucine zipper (HD-Zip) proteins. Plant Signal. Behav. 2009, 4:86-88.
45. Schrick K., et al. START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors. Genome Biol. 2004, 5:R41.
46. Mukherjee K., Bürglin T.R. MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins. Plant Physiol. 2006, 140:1142-1150.
47. Byrne M.E. Shoot meristem function and leaf polarity: the role of class III HD-ZIP genes. PLoS Genet. 2006, 2:e89.
48. Reitz J., et al. Cholesterol interaction with the related steroidogenic acute regulatory lipid-transfer (START) domains of StAR (STARD1) and MLN64 (STARD3). FEBS J. 2008, 275:1790-1802.
49. Tan Q.K., Irish V.F. The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development. Plant Physiol. 2006, 140:1095-1108.
50. Park H.C., et al. Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter. Nucleic Acids Res. 2007, 35:3612-3623.
51. Tran L.S., et al. Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J. 2007, 49:46-63.
52. Jin H., Martin C. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 1999, 41:577-585.
53. Simon M., et al. Distinct and overlapping roles of single-repeat MYB genes in root epidermal patterning. Dev. Biol. 2007, 311:566-578.
54. Tominaga R., et al. Functional analysis of the epidermal-specific MYB genes CAPRICE and WEREWOLF in Arabidopsis. Plant Cell 2007, 19:2264-2277.
55. Kirik V., et al. The ENHANCER OF TRY AND CPC1 gene acts redundantly with TRIPTYCHON and CAPRICE in trichome and root hair cell patterning in Arabidopsis. Dev. Biol. 2004, 268:506-513.
56. Matsui K., et al. AtMYBL2, a protein with a single MYB domain, acts as a negative regulator of anthocyanin biosynthesis in Arabidopsis. Plant J. 2008, 55:954-967.
57. Dubos C., et al. MYBL2 is a new regulator of flavonoid biosynthesis in Arabidopsis thaliana. Plant J. 2008, 55:940-953.
58. Chen C.H., et al. Affinity of synthetic peptide fragments of MyoD for Id1 protein and their biological effects in several cancer cells. J. Pept. Sci. 2010, 16:231-241.
59. Lingbeck J.M., et al. E12 and E47 modulate cellular localization and proteasome-mediated degradation of MyoD and Id1. Oncogene 2005, 24:6376-6384.
60. Coma S., et al. Id2 promotes tumor cell migration and invasion through transcriptional repression of semaphorin 3F. Cancer Res. 2010, 70:3823-3832.
61. Hyun Y., Lee I. KIDARI, encoding a non-DNA Binding bHLH protein, represses light signal transduction in Arabidopsis thaliana. Plant Mol. Biol. 2006, 61:283-296.
62. Duek P.D., Fankhauser C. HFR1, a putative bHLH transcription factor, mediates both phytochrome A and cryptochrome signalling. Plant J. 2003, 34:827-836.
63. Zhang X.N., et al. HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana. PLoS ONE 2008, 3:e3563.
64. Lorrain S., et al. Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light. Plant J. 2009, 60:449-461.
65. Hornitschek P., et al. Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers. EMBO J. 2009, 28:3893-3902.
66. Hu W., et al. Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families. J. Integr. Plant Biol. 2008, 50:1031-1045.
67. Hanada K., et al. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res. 2007, 17:632-640.
68. Stamm S., et al. Function of alternative splicing. Gene 2005, 344:1-20.
69. Li J., et al. A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J. Exp. Bot. 2006, 57:1263-1273.
70. Zou M., et al. Characterization of alternative splicing products of bZIP transcription factors OsABI5. Biochem. Biophys. Res. Commun. 2007, 360:307-313.
71. Roman C., et al. A dominant negative form of transcription activator mTFE3 created by differential splicing. Science 1991, 254:94-97.
72. Sasaki K., et al. Functional analysis of a dominant-negative ΔETS TEL/ETV6 isoform. Biochem. Biophys. Res. Commun. 2004, 317:1128-1137.
73. Kazan K. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 2003, 8:468-471.
74. Li L., et al. Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves. Plant J. 2009, 58:485-498.
75. van der Vaart M., Schaaf M.J. Naturally occurring C-terminal splice variants of nuclear receptors. Nucl. Recept. Signal. 2009, 7:e007.
76. Divi U.K., Krishna P. Brassinosteroid: a biotechnological target for enhancing crop yield and stress tolerance. New Biotechnol. 2009, 26:131-136.
77. Sato Y., et al. Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC Plant Biol. 2011, 11:10.
78. Yuan J.S., et al. Plants to power: bioenergy to fuel the future. Trends Plant Sci. 2008, 13:421-429.
79. Ma J., et al. The sucrose-regulated Arabidopsis transcription factor bZIP11 reprograms metabolism and regulates trehalose metabolism. New Phytol. 2011, 191:733-745.
80. Ambavaram M.M., et al. Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice. Plant Physiol. 2011, 155:916-931.
81. Valliyodan B., Nguyen H.T. Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Curr. Opin. Plant Biol. 2006, 9:189-195.
82. Xiang Y., et al. Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol. 2008, 148:1938-1952.
83. Hussain S.S., et al. Transcription factors as tools to engineer enhanced drought stress tolerance in plants. Biotechnol. Prog. 2011, 27:297-306.
84. Ossowski S., et al. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 2008, 53:674-690.
85. Frizzi A., Huang S. Tapping RNA silencing pathways for plant biotechnology. Plant Biotechnol. J. 2010, 8:655-677.
86. Schwab R., et al. Directed gene silencing with artificial microRNAs. Methods Mol. Biol. 2010, 592:71-88.
87. Small I. RNAi for revealing and engineering plant gene functions. Curr. Opin. Biotechnol. 2007, 18:148-153.
88. Nishimura N., et al. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 2009, 326:1373-1379.
89. Schaller G.E., Bleecker A.B. Ethylene-binding sites generated in yeast expressing the Arabidopsis ETR1 gene. Science 1995, 270:1809-1811.
90. Bhattacharjee A., et al. Deposition of stearate-oleate rich seed fat in Mangifera indica is mediated by a FatA type acyl-ACP thioesterase. Phytochemistry 2011, 72:166-177.
91. Dudkina N.V., et al. Structure of a mitochondrial supercomplex formed by respiratory-chain complexes I and III. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:3225-3229.