Structure and function of CW domain containing proteins

Current Protein and Peptide Science

Volumn 17, Issue 5, 2016, Pages 497-506

  Liu, Yanli ^a   Liu, Shasha ^a   Zhang, Xinxin ^b   Liang, Xiao ^a   Zahid, Kashif Rafiq ^a   Liu, Ke ^a   Liu, Jinlin ^a   Deng, Lingfu ^a   Yang, Jihong ^a   Qi, Chao ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

^b Dalian Vocational Technical College   (China)

Author keywords

CW domain; Early embryonic development; Epigenetic regulation; Transcription

Indexed keywords

CYSTEINE; HISTONE DEMETHYLASE; HISTONE METHYLTRANSFERASE; METHYL CPG BINDING PROTEIN 2; PROTEIN P53; TRYPTOPHAN; UNCLASSIFIED DRUG; ZCWPW1 PROTEIN; ZCWPW2 PROTEIN; ZINC FINGER PROTEIN; ARABIDOPSIS PROTEIN; CARRIER PROTEIN; HISTONE; PROTEIN BINDING; ZINC; ZINC-BINDING PROTEIN;

ARTICLE; CHEMICAL BINDING; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; DNA BINDING MOTIF; DNA METHYLATION; EMBRYO DEVELOPMENT; EPIGENETICS; FUNCTIONAL PROTEOMICS; GENE EXPRESSION REGULATION; GENE MUTATION; HUMAN; LARGE CELL LYMPHOMA; MOLECULAR DOCKING; NONHUMAN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROCESSING; SEED DEVELOPMENT; SEQUENCE ALIGNMENT; SPERMATOGENESIS; STRUCTURE ACTIVITY RELATION; TRIPLE NEGATIVE BREAST CANCER; VERTEBRATE; AMINO ACID SEQUENCE; BINDING SITE; CHEMISTRY; CONSERVED SEQUENCE; GENETICS; METABOLISM; MOLECULAR MODEL; MULTIGENE FAMILY; PROTEIN CONFORMATION; PROTEIN DOMAIN;

AMINO ACID SEQUENCE; ARABIDOPSIS PROTEINS; BINDING SITES; CARRIER PROTEINS; CONSERVED SEQUENCE; CYSTEINE; HISTONES; HUMANS; MODELS, MOLECULAR; MULTIGENE FAMILY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; STRUCTURE-ACTIVITY RELATIONSHIP; TRYPTOPHAN; ZINC;

EID: 84973658758     PISSN: 13892037     EISSN: 18755550     Source Type: Journal    
DOI: 10.2174/1389203717666160125115130     Document Type: Article

References (71)

1. Vaquero, A.; Loyola, A.; Reinberg, D. The constantly changing face of chromatin. Science's SAGE KE, 2003, 2003, 4.
2. Strahl, B.D.; Allis, C.D. The language of covalent histone modifications. Nature, 2000, 403, 41-45.
3. Hake, S.; Xiao, A.; Allis, C. Linking the epigenetic 'language'of covalent histone modifications to cancer. Br. J.Cancer, 2004, 90, 761-769.
4. Adams-Cioaba, M.A.; Min, J. Structure and function of histone methylation binding proteins Biochem. Cell Biol., 2009, 87, 93105.
5. Qin, S.; Min, J. Structure and function of the nucleosome-binding PWWP domain. Trends Biochem. Sci., 2014, 39, 536-547.
6. Xu, C.; Min, J. Structure and function of WD40 domain proteins. Protein Cell, 2011, 2, 202-214.
7. Guo, Y.; Nady, N.; Qi, C.; Allali-Hassani, A.; Zhu, H.; Pan, P.; Adams-Cioaba, M.A.; Amaya, M.F.; Dong, A.; Vedadi, M.; Schapira, M.; Read, R.J.; Arrowsmith, C.H.; Min, J. Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res., 2009, 37(7), 2204-2210.
8. Collins, R.E.; Northrop, J.P.; Horton, J.R.; Lee, D.Y.; Zhang, X.; Stallcup, M.R.; Cheng, X. The ankyrin repeats of G9a and GLP histone methyltransferases are mono-and dimethyllysine binding modules. Nat Struct. Mol. Biol., 2008, 15, 245-250.
9. Peña, P.V.; Davrazou, F.; Shi, X.; Walter, K.L.; Verkhusha, V.V.; Gozani, O.; Zhao, R.; Kutateladze, T.G. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature, 2006, 442(7098), 100-103.
10. Li, H.; Ilin, S.; Wang, W.; Duncan, E.M.; Wysocka, J.; Allis, C.D.; Patel, D.J. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature, 2006, 442(7098), 91-95.
11. Huang, Y.; Fang, J.; Bedford, M.T.; Zhang, Y.; Xu, R.-M. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science, 2006, 312, 748-751.
12. Flanagan, J.F.; Mi, L.-Z.; Chruszcz, M.; Cymborowski, M.; Clines, K.L.; Kim, Y.; Minor, W.; Rastinejad, F.; Khorasanizadeh, S. Dou- ble chromodomains cooperate to recognize the methylated histone H3 tail. Nature, 2005, 438, 1181-1185.
13. He, F.; Umehara, T.; Saito, K.; Harada, T.; Watanabe, S.; Yabuki, T.; Kigawa, T.; Takahashi, M.; Kuwasako, K.; Tsuda, K.; Matsuda, T.; Aoki, M.; Seki, E.; Kobayashi, N.; Güntert, P.; Yokoyama, S.; Muto, Y. Structural Insight into the Zinc Finger CW Domain as a Histone Modification Reader. Structure, 2010, 18, 1127-1139.
14. Hoppmann, V.; Thorstensen, T.; Kristiansen, P.E.; Veiseth, S.V.; Rahman, M.A.; Finne, K.; Aalen, R.B.; Aasland, R. The CW domain, a new histone recognition module in chromatin proteins. EMBO J., 2011, 30, 1939-1952.
15. Li, X.; Foley, E.A.; Molloy, K.R.; Li, Y.; Chait, B.T.; Kapoor, T.M. Quantitative Chemical Proteomics Approach To Identify Post-translational Modification-Mediated Protein-Protein Interactions. J. Am. Chem. Soc., 2012, 134, 1982-1985.
16. Perry, J.; Zhao, Y. The CW domain, a structural module shared amongst vertebrates, vertebrate-infecting parasites and higher plants. Trends Biochem. Sci., 2003, 28, 576-580.
17. Watson, M.L.; Zinn, A.R.; Inoue, N.; Hess, K.D.; Cobb, J.; Handel, M.A.; Halaban, R.; Duchene, C.C.; Albright, G.M.; Moreadith, R.W. Identification of morc (microrchidia), a mutation that results in arrest of spermatogenesis at an early meiotic stage in the mouse. Proc. Natl. Acad. Sci. U. S. A., 1998, 95, 14361-14366.
18. Inoue, N.; Hess, K.D.; Moreadith, R.W.; Richardson, L.L.; Handel, M.A.; Watson, M.L.; Zinn, A.R. New gene family defined by MORC, a nuclear protein required for mouse spermatogenesis. Hum. Mol Genet., 1999, 8, 1201-1207.
19. Kim, S.Y.; He, Y.; Jacob, Y.; Noh, Y.-S.; Michaels, S.; Amasino, R. Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell, 2005, 17, 3301-3310.
20. Ko, J.H.; Mitina, I.; Tamada, Y.; Hyun, Y.; Choi, Y.; Amasino, R.M.; Noh, B.; Noh, Y.S. Growth habit determination by the balance of histone methylation activities in Arabidopsis. EMBO J., 2010, 29, 3208-3215.
21. Li, D.-Q.; Nair, Sujit S.; Ohshiro, K.; Kumar, A.; Nair, V.S.; Pakala, S.B.; Reddy, S.D.; Gajula, R.P.; Eswaran, J.; Aravind, L.; Kumar, R. MORC2 Signaling Integrates Phosphorylation-Dependent, ATPase-Coupled Chromatin Remodeling during the DNA Damage Response. Cell Rep., 2012, 2, 1657-1669.
22. Zhou, Y.; Tan, B.; Luo, M.; Li, Y.; Liu, C.; Chen, C.; Yu, C.W.; Yang, S.; Dong, S.; Ruan, J.; Yuan, L.; Zhang, Z.; Zhao, L.; Li, C.; Chen, H.; Cui, Y.; Wu, K.; Huang, S. HISTONE DEACETY-LASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings. Plant Cell, 2013, 25, 134-148.
23. Veerappan, V.; Chen, N.; Reichert, A.I.; Allen, R.D. HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings. BMC Plant Biol., 2014, 14, 293.
24. Zhang, Q.; Qi, S.; Xu, M.; Yu, L.; Tao, Y.; Deng, Z.; Wu, W.; Li, J.; Chen, Z.; Wong, J. Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. Cell Res., 2012, 23, 225-241.
25. Fang, R.; Chen, F.; Dong, Z.; Hu, D.; Barbera, A.J.; Clark, E.A.; Fang, J.; Yang, Y.; Mei, P.; Rutenberg, M.; Li, Z.; Zhang, Y.; Xu, Y.; Yang, H.; Wang, P.; Simon, M.D.; Zhou, Q.; Li, J.; Marynick, M.P.; Li, X.; Lu, H.; Kaiser, U.B.; Kingston, R.E.; Xu, Y.; Shi, Y.G. LSD2/KDM1B and Its Cofactor NPAC/GLYR1 Endow a Structural and Molecular Model for Regulation of H3K4 Demethylation. Mol. Cell, 2013, 49, 558-570.
26. Liggins, A.P.; Cooper, C.D.O.; Lawrie, C.H.; Brown, P.J.; Collins, A. P.; Hatton, C.S.; Pulford, K.; Banham, A.H. MORC4, a novel member of the MORC family, is highly expressed in a subset of diffuse large B-cell lymphomas. Br. J. Haematol., 2007, 138, 479-486.
27. Karytinos, A.; Forneris, F.; Profumo, A.; Ciossani, G.; Battaglioli, D.; Binda, C.; Mattevi, A. A novel mammalian flavin-dependent histone demethylase. J. Biol. Chem., 2009, 284, 17775-17782.
28. Shah, S.P.; Morin, R.D.; Khattra, J.; et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 2009, 461, 809-813.
29. Fang, R.; Barbera, A.J.; Xu, Y.; Rutenberg, M.; Leonor, T.; Bi, Q.; Lan, F.; Mei, P.; Yuan, G.C.; Lian, C.; Peng, J.; Cheng, D.; Sui, G.; Kaiser, U.B.; Shi, Y.; Shi, Y.G. Human LSD2/KDM1b/AOF1 Regulates Gene Transcription by Modulating Intragenic H3K4me2 Methylation. Mol. Cell, 2010, 39, 222-233.
30. Shao, Y.; Li, Y.; Zhang, J.; Liu, D.; Liu, F.; Zhao, Y.; Shen, T.; Li, E. Involvement of histone deacetylation in MORC2-mediated down-regulation of carbonic anhydrase IX. Nucleic Acids Res., 2010, 38, 2813-2824.
31. Yang, Z.; Jiang, J.; Stewart, D.M.; Qi, S.; Yamane, K.; Li, J.; Zhang, Y.; Wong, J. AOF1 is a histone H3K4 demethylase possessing demethylase activity-independent repression function. Cell Res., 2010, 20, 276-287.
32. Chen, L.H.; Kuo, W.-H.; Tsai, M.-H.; Chen, P.C.; Hsiao, C.K.; Chuang, E.Y.; Chang, L.Y.; Hsieh, F.J.; Lai, L.C.; Chang, K.J. Identification of prognostic genes for recurrent risk prediction in triple negative breast cancer patients in Taiwan. PLoS One., 2011, 6(11), e28222.
33. van Essen, D.; Zhu, Y.; Saccani, S. A feed-forward circuit controlling inducible NF-κB target gene activation by promoter histone demethylation. Mol. cell, 2010, 39, 750-760.
34. Ciccone, D.N.; Su, H.; Hevi, S.; Gay, F.; Lei, H.; Bajko, J.; Xu, G.; Li, E.; Chen, T. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature, 2009, 461, 415-418.
35. Iyer, L.M.; Abhiman, S.; Aravind, L. MutL homologs in restriction-modification systems and the origin of eukaryotic MORC AT-Pases. Biol. Direct, 2008, 3, 8.
36. Nagase, T.; Ishikawa, K.-i.; Suyama, M.; Kikuno, R.; Hirosawa, M.; Miyajima, N.; Tanaka, A.; Kotani, H.; Nomura, N.; Ohara, O. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res., 1998, 5, 355-364.
37. Takahashi, K.; Yoshida, N.; Murakami, N.; Kawata, K.; Ishizaki, B.; Tanaka-Okamoto, M.; Miyoshi, J.; Zinn, A.R.; Shime, H.; Inoue, N. Dynamic Regulation of p53 Subnuclear Localization and Senescence by MORC3. Mol. Biol. Cell, 2007, 18, 1701-1709.
38. Kimura, Y.; Sakai, F.; Nakano, O.; Kisaki, O.; Sugimoto, H.; Sawamura, T.; Sadano, H.; Osumi, T. The Newly Identified Human Nuclear Protein NXP-2 Possesses Three Distinct Domains, the Nuclear Matrix-binding, RNA-binding, and Coiled-coil Domains. J. Biol. Chem., 2002, 277, 20611-20617.
39. González-Fernández, R.; Morales, M.; Avila, J.; Martín-Vasallo, P. Changes in leukocyte gene expression profiles induced by antineoplastic chemotherapy. Oncol. Lett., 2012, 3, 1341-1349.
40. Zhao, Z.; Yu, Y.; Meyer, D.; Wu, C.; Shen, W.-H. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat. Cell Biol., 2005, 7, 1256-1260.
41. Xu, L.; Zhao, Z.; Dong, A.; Soubigou-Taconnat, L.; Renou, J.P.; Steinmetz, A.; Shen, W.H. Di-and tri-but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol. Cell. Biol., 2008, 28, 1348-1360.
42. Soppe, W.J.; Bentsink, L.; Koornneef, M. The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana, Development 126, 4763-4770. Development, 1997, 126, 4763-4777.
43. Tang, X.; Lim, M.H.; Pelletier, J.; Tang, M.; Nguyen, V.; Keller, W.A.; Tsang, E.W.; Wang, A.; Rothstein, S.J.; Harada, J.J.; Cui, Y. Synergistic repression of the embryonic programme by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis seedlings. J. Exp. Bot., 2012, 63, 1391-1404.
44. Dong, G.; Ma, D.-P.; Li, J. The histone methyltransferase SDG8 regulates shoot branching in Arabidopsis. Biochem. Biophys. Res. Commun., 2008, 373, 659-664.
45. Grini, P.E.; Thorstensen, T.; Alm, V.; Vizcay-Barrena, G.; Windju, S.S.; Jørstad, T.S.; Wilson, Z.A.; Aalen, R.B. The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis. PLoS One, 2009, 4, e7817-e7817.
46. Julie, A.L.; Steven, E.J. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet., 2010, 11, 204-220.
47. He, X.J.; Chen, T.; Zhu, J.K. Regulation and function of DNA methylation in plants and animals. Cell Res., 2011, 21, 442-465.
48. Richards, E.J. DNA methylation and plant development. Trends Genet., 1997, 13, 319-323.
49. Hendrich, B.; Bird, A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol., 1998, 18, 6538-6547.
50. Bird, A.P.; Wolffe, A.P. Methylation-induced repression--belts, braces, and chromatin. Cell, 1999, 99, 451-454.
51. Springer, N.M.; Kaeppler, S.M. Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. Plant Physiol., 2004, 138, 92-104.
52. Anita, B.; Meza, T.J.; Mirela, M.; Tage, T.; Kjetil, K.; Aalen, R.B. Ten members of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development. Nucleic Acids Res., 2003, 31, 5291-5304.
53. Zemach, A.; Grafi, G. Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci., 2007, 12, 80-85.
54. Zemach, A.; Grafi, G. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J., 2003, 34, 565-572.
55. Ito, M.; Koike, A.; Koizumi, N.; Sano, H. Methylated DNA-binding proteins from Arabidopsis. Plant Physiol., 2003, 133, 1747-1754.
56. Assaf, Z.; Yan, L.; Bess, W.; Ben-Meir, H.; Kiss, V.; Avivi, Y.; Kalchenko, V.; Jacobsen, S.E.; Grafi, G. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. Plant Cell, 2005, 17, 1549-1558.
57. Peng, M.; Cui, Y.; Bi, Y.M.; Rothstein, S.J. AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis. Plant J., 2006, 46, 282-296.
58. Giraudat, J.; Hauge, B.M.; Valon, C.; Smalle, J.; Parcy, F.; Goodman, H.M. Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell, 1992, 4, 1251-1261.
59. Lotan, T.; Ohto, M.; Yee, K.M.; West, M.A.; Lo, R.; Kwong, R.W.; Yamagishi, K.; Fischer, R.L.; Goldberg, R.B.; Harada, J.J. Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell, 1998, 93, 1195-1205.
60. Luerssen, H.; Kirik, V.; Herrmann, P.; Misera, S. FUSCA3 encodes a protein with a conserved VP1/AB13-like B3 domain which is of functional importance for the regulation of seed maturation in Arabidopsis thaliana. Plant J., 1998, 15, 755-764.
61. Stone, S.L.; Kwong, L.W.; Yee, K.M.; Pelletier, J.; Lepiniec, L.; Fischer, R.L.; Goldberg, R.B.; Harada, J.J. LEAFY COTYLE-DON2 encodes a B3 domain transcription factor that induces em bryo development. Proc. Natl. Acad. Sci. U. S. A., 2001, 98, 11806-11811.
62. Kwong, R.W.; Bui, A.Q.; Lee, H.; Kwong, L.W.; Fischer, R.L.; Goldberg, R.B.; Harada, J.J. LEAFY COTYLEDON1-LIKE defines a class of regulators essential for embryo development. Plant Cell, 2003, 15, 5-18.
63. Suzuki, M.; Wang, H.H.; McCarty, D.R. Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol., 2007, 143, 902-911.
64. Jia, H.; Suzuki, M.; McCarty, D.R. Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks. Wiley Interdiscip. Rev. Dev. Biol., 2014, 3, 135-145.
65. Tsukagoshi, H.; Morikami, A.; Nakamura, K. Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings. Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 2543-2547.
66. Veerappan, V.; Wang, J.; Kang, M.; Lee, J.; Tang, Y.; Jha, A.K.; Shi, H.; Palanivelu, R.; Allen, R.D. A novel HSI2 mutation in Arabidopsis affects the PHD-like domain and leads to derepression of seed-specific gene expression. Planta, 2012, 236, 1-17.
67. Tsukagoshi, H.; Saijo, T.; Shibata, D.; Morikami, A.; Nakamura, K. Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor. Plant Physiol., 2005, 138, 675-685.
68. Lan, F.; Collins, R.E.; De Cegli, R.; Alpatov, R.; Horton, J.R.; Shi, X.; Gozani, O.; Cheng, X.; Shi, Y. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature, 2007, 448, 718-722.
69. Sigrist, C.J.; Cerutti, L.; De Castro, E.; Langendijk-Genevaux, P.S.; Bulliard, V.; Bairoch, A.; Hulo, N. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res., 2010, 38, D161-D166.
70. Qin, S.; Liu, Y.; Tempel, W.; Eram, M.S.; Bian, C.; Liu, K.; Senisterra, G.; Crombet, L.; Vedadi, M.; Min, J. Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1. Nat.Commun., 2014, 5, 3952.
71. Thompson, J.D.; Higgins, D.G.; Gibson, T.J. Clustal, W. improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nudeic Acids Res., 1994, 22, 4673-4680.