Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 27, 2011, Pages 11157-11162

  Krichevsky, Alexander ^a   Zaltsman, Adi ^a   Lacroix, Benoît ^a   Citovsky, Vitaly ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

Bimolecular fluorescence complementation; Otubain superfamily; Repression of gene expression

Indexed keywords

ARABIDOPSIS PROTEIN; HISTONE DEMETHYLASE; HISTONE H2B; OTUBAIN LIKE DEUBIQUITINASE; PROTEIN KDM1C; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; CHROMATIN; GENE CONTROL; GENE EXPRESSION; GENE REPRESSION; GENE SILENCING; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE UBIQUITINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; CHROMATIN; CYSTEINE PROTEASES; DNA PRIMERS; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HISTONE DEMETHYLASES; HISTONES; MOLECULAR SEQUENCE DATA; MULTIENZYME COMPLEXES; PLANTS, GENETICALLY MODIFIED; RECOMBINANT PROTEINS; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TWO-HYBRID SYSTEM TECHNIQUES; UBIQUITINATION;

ANIMALIA; ARABIDOPSIS;

EID: 79960582700     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1014030108     Document Type: Article

References (64)

1. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074-1080. (Pubitemid 32758077)
2. Kadonaga JT (1998) Eukaryotic transcription: An interlaced network of transcription factors and chromatin-modifying machines. Cell 92:307-313.
3. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41-45. (Pubitemid 30038513)
4. Carrozza MJ, Utley RT, Workman JL, Côté J (2003) The diverse functions of histone acetyltransferase complexes. Trends Genet 19:321-329. (Pubitemid 36694615)
5. Goodrich J, Tweedie S (2002) Remembrance of things past: Chromatin remodeling in plant development. Annu Rev Cell Dev Biol 18:707-746. (Pubitemid 35387365)
6. Aravind L, Iyer LM (2002) The SWIRM domain: A conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biol 3:research0039.0031-0039.0037.
7. Shi Y, et al. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-953. (Pubitemid 40037608)
8. Krichevsky A, et al. (2007) C2H2 zinc finger-SET histone methyltransferase is a plantspecific chromatin modifier. Dev Biol 303:259-269. (Pubitemid 46241103)
9. Krichevsky A, Kozlovsky SV, Gutgarts H, Citovsky V (2007) Arabidopsis co-repressor complexes containing polyamine oxidase-like proteins and plant-specific histone methyltransferases. Plant Signal Behav 2:174-177. (Pubitemid 351280319)
10. Jepsen K, Rosenfeld MG (2002) Biological roles and mechanistic actions of corepressor complexes. J Cell Sci 115:689-698. (Pubitemid 34196329)
11. Ballas N, Grunseich C, Lu DD, Speh JC, Mandel G (2005) REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121:645-657. (Pubitemid 40720016)
12. Lunyak VV, Prefontaine GG, Rosenfeld MG (2004) REST and peace for the neuronalspecific transcriptional program. Ann N Y Acad Sci 1014:110-120. (Pubitemid 38594796)
13. Cao R, et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039-1043. (Pubitemid 35247314)
14. Rea S, et al. (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406:593-599. (Pubitemid 30641039)
15. Tsukada Y, et al. (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439:811-816. (Pubitemid 43255695)
16. Vissers JH, Nicassio F, van Lohuizen M, Di Fiore PP, Citterio E (2008) The many faces of ubiquitinated histone H2A: Insights from the DUBs. Cell Div 3:8.
17. Weake VM, Workman JL (2008) Histone ubiquitination: Triggering gene activity. Mol Cell 29:653-663. (Pubitemid 351400924)
18. Henry KW, et al. (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev 17:2648-2663. (Pubitemid 37363070)
19. Zhang Y (2003) Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev 17:2733-2740.
20. Sridhar VV, et al. (2007) Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447:735-738. (Pubitemid 46889731)
21. Nickel BE, Allis CD, Davie JR (1989) Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin. Biochemistry 28:958-963.
22. van der Knaap JA, et al. (2005) GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Mol Cell 17:695-707.
23. Zhang K, Sridhar VV, Zhu J, Kapoor A, Zhu JK (2007) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS ONE 2:e1210.
24. Gu X, Jiang D, Wang Y, Bachmair A, He Y (2009) Repression of the floral transition via histone H2B monoubiquitination. Plant J 57:522-533.
25. Cao Y, Dai Y, Cui S, Ma L (2008) Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell 20: 2586-2602. (Pubitemid 352844578)
26. Luo M, et al. (2008) UBIQUITIN-SPECIFIC PROTEASE 26 is required for seed development and the repression of PHERES1 in Arabidopsis. Genetics 180:229-236.
27. Doelling JH, Yan N, Kurepa J, Walker J, Vierstra RD (2001) The ubiquitin-specific protease UBP14 is essential for early embryo development in Arabidopsis thaliana. Plant J 27:393-405. (Pubitemid 32943819)
28. Makarova KS, Aravind L, Koonin EV (2000) A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem Sci 25:50-52. (Pubitemid 30100365)
29. Balakirev MY, Tcherniuk SO, Jaquinod M, Chroboczek J (2003) Otubains: A new family of cysteine proteases in the ubiquitin pathway. EMBO Rep 4:517-522. (Pubitemid 36789851)
30. Komander D, Barford D (2008) Structure of the A20 OTU domain and mechanistic insights into deubiquitination. Biochem J 409:77-85.
31. Aquea F, Gutiérrez F, Medina C, Arce-Johnson P (2008) A novel Otubain-like cysteine protease gene is preferentially expressed during somatic embryogenesis in Pinus radiata. Mol Biol Rep 35:567-573.
32. Hofmann K, Bucher P (1996) The UBA domain: A sequence motif present in multiple enzyme classes of the ubiquitination pathway. Trends Biochem Sci 21:172-173. (Pubitemid 126335285)
33. Bartel P, Chien CT, Sternglanz R, Fields S (1993) Elimination of false positives that arise in using the two-hybrid system. Biotechniques 14:920-924. (Pubitemid 23166805)
34. Hollenberg SM, Sternglanz R, Cheng PF, Weintraub H (1995) Identification of a new family of tissue-specific basic helix-loop-helix proteins with a two-hybrid system. Mol Cell Biol 15:3813-3822.
35. Hu CD, Chinenov Y, Kerppola TK (2002) Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 9:789-798. (Pubitemid 34454889)
36. Citovsky V, et al. (2006) Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta. J Mol Biol 362:1120-1131. (Pubitemid 44353530)
37. Citovsky V, Gafni Y, Tzfira T (2008) Localizing protein-protein interactions by bimolecular fluorescence complementation in planta. Methods 45:196-206.
38. Tzfira T, Vaidya M, Citovsky V (2004) Involvement of targeted proteolysis in plant genetic transformation by Agrobacterium. Nature 431:87-92. (Pubitemid 39215113)
39. He Y, Michaels SD, Amasino RM (2003) Regulation of flowering time by histone acetylation in Arabidopsis. Science 302:1751-1754. (Pubitemid 37505736)
40. Krichevsky A, Zaltsman A, Kozlovsky SV, Tian GW, Citovsky V (2009) Regulation of root elongation by histone acetylation in Arabidopsis. J Mol Biol 385:45-50.
41. Bergmüller E, Gehrig PM, Gruissem W (2007) Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana. J Proteome Res 6:3655-3668. (Pubitemid 47522755)
42. Jiang D, Yang W, He Y, Amasino RM (2007) Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell 19:2975-2987. (Pubitemid 350276706)
43. Zhou X, Ma H (2008) Evolutionary history of histone demethylase families: Distinct evolutionary patterns suggest functional divergence. BMC Evol Biol 8:294.
44. Ardley HC, Robinson PA (2005) E3 ubiquitin ligases. Essays Biochem 41:15-30. (Pubitemid 41500968)
45. Dover J, et al. (2002) Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277:28368-28371.
46. Lee JS, et al. (2007) Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell 131:1084-1096.
47. Sun ZW, Allis CD (2002) Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418:104-108.
48. Zhu B, et al. (2005) Monoubiquitination of human histone H2B: The factors involved and their roles in HOX gene regulation. Mol Cell 20:601-611. (Pubitemid 41668644)
49. Rudolph T, et al. (2007) Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3. Mol Cell 26: 103-115. (Pubitemid 46566423)
50. Alonso JM, et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653-657. (Pubitemid 36927950)
51. Citovsky V, Wong ML, Zambryski PC (1989) Cooperative interaction of Agrobacterium VirE2 protein with single-stranded DNA: Implications for the T-DNA transfer process. Proc Natl Acad Sci USA 86:1193-1197.
52. Citovsky V, DE Vos G, Zambryski PC (1988) Single-stranded DNA binding protein encoded by the virE locus of Agrobacterium tumefaciens. Science 240:501-504.
53. Lacroix B, Loyter A, Citovsky V (2008) Association of the Agrobacterium T-DNAprotein complex with plant nucleosomes. Proc Natl Acad Sci USA 105:15429-15434.
54. Iakoucheva LM, et al. (2001) Aberrant mobility phenomena of the DNA repair protein XPA. Protein Sci 10:1353-1362. (Pubitemid 32568102)
55. Bowler C, et al. (2004) Chromatin techniques for plant cells. Plant J 39:776-789. (Pubitemid 39218784)
56. Gabrielli F, et al. (1984) Histone complements of human tissues, carcinomas, and carcinoma-derived cell lines. Mol Cell Biochem 65:57-66. (Pubitemid 15218496)
57. Sutton A, et al. (2001) A novel form of transcriptional silencing by Sum1-1 requires Hst1 and the origin recognition complex. Mol Cell Biol 21:3514-3522. (Pubitemid 32381787)
58. Ballas N, Citovsky V (1997) Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Agrobacterium VirD2 protein. Proc Natl Acad Sci USA 94:10723-10728. (Pubitemid 27430801)
59. Tzfira T, Vaidya M, Citovsky V (2001) VIP1, an Arabidopsis protein that interacts with Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. EMBO J 20:3596-3607. (Pubitemid 32634366)
60. Tzfira T, Vaidya M, Citovsky V (2002) Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis VIP1 gene. Proc Natl Acad Sci USA 99:10435-10440.
61. SenGupta DJ, et al. (1996) A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci USA 93:8496-8501. (Pubitemid 26269587)
62. Tzfira T, et al. (2005) pSAT vectors: A modular series of plasmids for autofluorescent protein tagging and expression of multiple genes in plants. Plant Mol Biol 57:503-516. (Pubitemid 40588707)
63. Ueki S, Lacroix B, Krichevsky A, Lazarowitz SG, Citovsky V (2009) Functional transient genetic transformation of Arabidopsis leaves by biolistic bombardment. Nat Protoc 4:71-77.
64. Johnson L, Cao X, Jacobsen S (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12:1360-1367.