Structural studies on MRG701 chromodomain reveal a novel dimerization interface of MRG proteins in green plants

Yanchao Liu, Hong Wu, Yu Yu, Ying Huang

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Protein Cell ›› 2016, Vol. 7 ›› Issue (11) : 792-803. DOI: 10.1007/s13238-016-0310-5
RESEARCH ARTICLE
RESEARCH ARTICLE

Structural studies on MRG701 chromodomain reveal a novel dimerization interface of MRG proteins in green plants

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Abstract

MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701CD). MRG701CD forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants. Our findings may provide new insights into the mechanism of MRGs in regulation of gene expression in green plants.

Keywords

MRG701 / chromodomain / homodimer

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Yanchao Liu, Hong Wu, Yu Yu, Ying Huang. Structural studies on MRG701 chromodomain reveal a novel dimerization interface of MRG proteins in green plants. Protein Cell, 2016, 7(11): 792‒803 https://doi.org/10.1007/s13238-016-0310-5

References

[1]
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, G’Kunstleve RW (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr Sect D 66:213–221
CrossRef Google scholar
[2]
Bannister AJ, Schneider R, Myers FA, Thorne AW, Crane-Robinson C, Kouzarides T (2005) Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J Biol Chem 280:17732–17736
CrossRef Google scholar
[3]
Bertram MJ, P’Smith OM (2001) Conservation of the MORF4 related gene family: identification of a new chromo domain subfamily and novel protein motif. Gene 266:111–121
CrossRef Google scholar
[4]
Bertram MJ, B�rub� NG, Hang-Swanson X, Ran Q, Leung JK, Bryce S, Spurgers K, Bick RJ, Baldini A, Ning Y (1999) Identification of a gene that reverses the immortal phenotype of a subset of cells and is a member of a novel family of transcription factor-like genes. Mol Cell Biol 19:1479–1485
CrossRef Google scholar
[5]
Brunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2:2728–2733
CrossRef Google scholar
[6]
Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, G’Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54:905–921
CrossRef Google scholar
[7]
Bu Z, Yu Y, Li Z, Liu Y, Jiang W, Huang Y, Dong AW (2014) Regulation of Arabidopsis flowering by the histone mark readers MRG1/2 via interaction with CONSTANS to modulate FT expression. PLoS Genet 10:e1004617
CrossRef Google scholar
[8]
Canzio D, Liao M, Naber N, Pate E, Laron A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R (2013) A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly. Nature 496:377–381
CrossRef Google scholar
[9]
Canzio D, Larson A, Narlikar GJ (2014) Mechanisms of functional promiscuity by HP1 proteins. Trends Cell Biol 24:377–386
CrossRef Google scholar
[10]
Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V, Koomen JM, Bedford MT, Zhang X (2011) MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nat Commun 2:533
CrossRef Google scholar
[11]
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D 66:486–501
CrossRef Google scholar
[12]
Gorman M, Franke A, Baker BS (1995) Molecular characterization of the male-specific lethal-3 gene and investigations of the regulation of dosage compensation in Drosophila. Development 121:463–475
[13]
Hayakawa T, Zhang F, Hayakawa N, Ohtani Y, Shinmyozu K, Nakayama J, Andreassen PR (2010) MRG15 binds directly to PALB2 and stimulates homology-directed repair of chromosomal breaks. J Cell Sci 123:1124–1130
CrossRef Google scholar
[14]
Hilfiker A, Hilfiker-Kleiner D, Pannuti A, Lucchesi JC (1997) mof, a putative acetyl transferase gene related to the Tip60 and MOZ human genes and to the SAS gene of yeast, is required for dosage compensation in Drosophila. EMBO J 16:2054–2060
CrossRef Google scholar
[15]
Jin J, Shi J, Liu B, Liu Y, Huang Y, Yu Y, Dong AW (2015) MORFRELATED GENE702, a reader protein of trimethylated histone H3 lysine 4 and histone H3 lysine 36, is involved in brassinosteroid- regulated growth and flowering time control in rice. Plant Physiol 168:1275–1285
CrossRef Google scholar
[16]
Kaustov L, Ouyang H, Amaya M, Lemak A, Nady N, Duan S, Wasney GA, Li Z, Vedadi M, Schapira M (2011) Recognition and specificity determinants of the human cbx chromodomains. J Biol Chem 286:521–529
CrossRef Google scholar
[17]
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J (2009) Differrential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41:376–381
CrossRef Google scholar
[18]
Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI (2007) MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell 28:121–133
CrossRef Google scholar
[19]
Leung JK, Berube N, Venable S, Ahmed S, Timchenko N, Pereira-Smith OM (2001) MRG15 activates the B-myb promoter through formation of a nuclear complex with the retinoblastoma protein and the novel protein PAM14. J Biol Chem 276:39171–39178
CrossRef Google scholar
[20]
Li J, Li Z, Ruan J, Xu C, Tong Y, Pan PW, Tempel W, Crombet L, Min J, Zang J (2011) Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9. PLoS One 6:e25104
CrossRef Google scholar
[21]
Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T(2010) Regulation of alternative splicing by histone modifications. Science 327:996–1000
CrossRef Google scholar
[22]
McCoy AJ, G’Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674
CrossRef Google scholar
[23]
Min J, Zhang Y, Xu RM (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17:1823–1828
CrossRef Google scholar
[24]
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326
CrossRef Google scholar
[25]
Pardo PS, Leung JK, Lucchesi JC, P’Smith OM (2002) MRG15, a novel chromodomain protein, is present in two distinct multiprotein complexes involved in transcriptional activation. J Biol Chem 277:50860–50866
CrossRef Google scholar
[26]
Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122:517–527
CrossRef Google scholar
[27]
Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factor. Cell 80:847–857
CrossRef Google scholar
[28]
Roudier F, Ahmed I, Berard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Cailieux E, Duvernois-Berthet E, Al-Shikhley L (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30:1928–1938
CrossRef Google scholar
[29]
Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613–1616
CrossRef Google scholar
[30]
Searle I, He Y, Turck F, Vincent C, Fornara F, Krober S, Amasino RA, Coupland G (2006) The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev 20:898–912
CrossRef Google scholar
[31]
Sun B, Hong J, Zhang P, Dong X, Shen X, Lin D, Ding J (2008) Molecular basis of the interaction of Saccharomyces cerevisiae Eaf3 chromo domain with methylated H3K36. J Biol Chem 283:36504–36512
CrossRef Google scholar
[32]
Tominaga K, Kirtane B, Jackson JG, Ikeno Y, Ikeda T, Hawks C, Smith JR, Matzuk MM, P’Smith OM (2005) MRG15 regulates embryonic development and cell proliferation. Mol Cell Biol 25:2924–2937
CrossRef Google scholar
[33]
Wyatt PJ (1993) Light scattering and the absolute characterization of macromolecules. Anal Chim Acta 272:1–40
CrossRef Google scholar
[34]
Xie T, Zmyslowski AM, Zhang Y, Radhakrishnan I(2015) Structural basis for multi-specificity of MRG domains. Structure 23:1049–1057
CrossRef Google scholar
[35]
Xu Y, Gan ES, Zhou J, Wee WY, Zhang X, Ito T (2014) Arabidopsis MRG domain proteins bridge two histone modifications to elevate expression of flowering genes. Nucleic Acids Res 42:10960–10974
CrossRef Google scholar
[36]
Yap KL, Zhou MM (2011) Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription. Biochemistry 50:1966–1980
CrossRef Google scholar
[37]
Yochum GS, Ayer DE (2002) Role for the mortality factors MORF4, MRGX, and MRG15 in transcriptional repression via associations with Pf1, mSin3A, and Transducin-Like Enhancer of Split. Mol Cell Biol 22:7868–7876
CrossRef Google scholar
[38]
Yu B, Cassani M, Wang M, Liu M, Ma J, Li G, Zhang Z, Huang Y (2015) Structural insights into Rhino-mediated germline piRNA cluster formation. Cell Res 25:525–528
CrossRef Google scholar
[39]
Zhang P, Du J, Sun B, Dong X, Xu G, Zhou J, Huang Q, Liu Q, Hao Q, Ding J (2006a) Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res 34:6621–6628
CrossRef Google scholar
[40]
Zhang P, Zhao J, Wang B, Du J, Lu Y, Chen J, Ding J (2006b) The MRG domain of human MRG15 uses a shallow hydrophobic pocket to interact with the N-terminal region of PAM14. Protein Sci 15:2423–2434
CrossRef Google scholar
[41]
Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10:1–14
CrossRef Google scholar

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2016 The Author(s) 2016. This article is published with open access at Springerlink.com and journal.hep.com.cn
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