[1] | Park NI, Muench DG (2007) Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14. Planta 225: 625–639.
|
[2] | Lee HC, Choe J, Chi SG, Kim YK (2009) Exon junction complex enhances translation of spliced mRNAs at multiple steps. Biochem Biolphys Res Cummun 384: 334–340.
|
[3] | Ashton-Beaucage D, Udell CM, Lavoie H, Baril C, Lefran?ois M, et al. (2010) The exon junction complex controls the splicing of mapk and other long intron-containing transcripts in Drosophila. Cell 143: 251–262.
|
[4] | Roignant JY, Treisman JE (2010) Exon junction complex subunits are required to splice Drosophila MAP kinase, a large heterochromatic gene. Cell 143: 238–250.
|
[5] | Boothby TC, Wolniak SM (2011) Masked mRNA is stored with aggregated nuclear speckles and its asymmetric redistribution requires a homolog of mago nashi. BMC Cell Biol 12: 45.
|
[6] | Mufarrege EF, Gonzalez DH, Curi GC (2011) Functional interconnections of Arabidopsis exon junction complex proteins and genes at multiple steps of gene expression. J Exp Bot 62: 5025–5036.
|
[7] | Zhao XF, Nowak NJ, Shows TB, Aplan PD (2000) MAGOH interacts with a novel RNA-binding protein. Genomics 63: 145–148.
|
[8] | Kim VN, Yong J, Kataoka N, Abel L, Diem MD, et al. (2001) The Y14 protein communicates to the cytoplasm the position of exon-exon junctions. EMBO J 20: 2062–2068.
|
[9] | Le Hir H, Gatfield D, Braun IC, Forler D, Izaurralde E (2001) The protein Mago provides a link between splicing and mRNA localization. EMBO Rep 2: 1119–1124.
|
[10] | Mohr SE, Dillon ST, Boswell RE (2001) The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis. Genes Dev 15: 2886–2899.
|
[11] | Palacios IM, Gatfield D, St Johnston D, Izaurralde E (2004) An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427: 753–757.
|
[12] | Park NI, Yeung EC, Muench DG (2009) Mago Nashi is involved in meristem organization, pollen formation, and seed development in Arabidopsis. Plant Sci 176: 461–469.
|
[13] | Kataoka N, Diem MD, Kim VN, Yong J, Dreyfuss G (2001) Magoh, a human homolog of Drosophila mago nashi protein, is a component of the splicing-dependent exon-exon junction complex. EMBO J 20: 6424–6433.
|
[14] | Kataoka N, Yong J, Kim VN, Velazquez F, Perkinson RA, et al. (2000) Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol Cell 6: 673–682.
|
[15] | Shi H, Xu RM (2003) Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes Dev 17: 971–976.
|
[16] | Newmark PA, Boswell RE (1994) The mago nashi locus encodes an essential product required for germ plasm assembly in Drosophila. Development 120: 1303–1313.
|
[17] | Newmark PA, Mohr SE, Gong L, Boswell RE (1997) mago nashi mediates the posterior follicle cell-to-oocyte signal to organize axis formation in Drosophila. Development 124: 3197–3207.
|
[18] | Micklem DR, Dasgupta R, Elliott H, Gergely F, Davidson C, et al. (1997) The mago nashi gene is required for the polarisation of the oocyte and the formation of perpendicular axes in Drosophila. Curr Biol 7: 468–478.
|
[19] | Parma DH, Bennett PE Jr, Boswell RE (2007) Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification. Dev Biol 308(2): 507–519.
|
[20] | Li W, Boswell R, Wood WB (2000) mag-1, a homolog of Drosophila mago nashi, regulates hermaphrodite germ-line sex determination in Caenorhabditis elegans. Dev Biol 218: 172–182.
|
[21] | Inaki M, Kato D, Utsugi T, Onoda F, Hanaoka F, et al. (2011) Genetic analyses using a mouse cell cycle mutant identifies magoh as a novel gene involved in Cdk regulation. Genes Cells 16: 166–178.
|
[22] | He CY, Sommer H, Grosardt B, Huijser P, Saedler H (2007) PFMAGO, a MAGO NASHI-like factor, interacts with the MADS-box protein MPF2 from Physalis floridana. Mol Biol Evol 24: 1229–1241.
|
[23] | Johnson MA, von Besser K, Zhou Q, Smith E, Aux G, et al. (2004) Arabidopsis hapless mutations define essential gametophytic functions. Genetics 168: 971–982.
|
[24] | van der Weele CM, Tsai CW, Wolniak SM (2007) Mago nashi is essential for spermatogenesis in Marsilea. Mol Biol Cell 18: 3711–3722.
|
[25] | Chen YR, Shaw JF, Chung MC, Chu FH (2007) Molecular identification and characterization of Tcmago and TcY14 in Taiwania (Taiwania cryptomerioides). Tree Physiol 27: 1261–1271.
|
[26] | Hachet O, Ephrussi A (2001) Drosophila Y14 shuttles to the posterior of the oocyte and is required for oskar mRNA transport. Curr Biol 11: 1666–1674.
|
[27] | Kawano T, Kataoka N, Dreyfuss G, Sakamoto H (2004) Ce-Y14 and MAG-1, components of the exon-exon junction complex, are required for embryogenesis and germline sexual switching in Caenorhabditis elegans. Mech Dev 121: 27–35.
|
[28] | Chu FH, Chen YR, Lee CH, Chang TT (2009) Molecular characterization and expression analysis of Acmago and AcY14 in Antrodia cinnamomea. Mycol Res 113: 577–582.
|
[29] | Liu M, Wang X, Lei L, Zhao Z, Shen J (2010) The identification, expression profile, and preliminary characterization of Tsunagi protein from Schistosoma japonicum. Parasitol Res 107: 615–621.
|
[30] | Lau CK, Diem MD, Dreyfuss G, Van Duyne GD (2003) Structure of the Y14-Magoh core of the exon junction complex. Curr Biol 13: 933–941.
|
[31] | Lewandowski JP, Sheehan KB, Bennett PE Jr, Boswell RE (2010) Mago Nashi, Tsunagi/Y14, and Ranshi form a complex that influences oocyte differentiation in Drosophila melanogaster. Dve Biol 339: 307–319.
|
[32] | Fribourg S, Gatfield D, Izaurralde E, Conti E (2003) A novel mode of RBD-protein recognition in the Y14–Mago complex. Nat Struct Biol 10: 433–439.
|
[33] | Ehrlich PR, Raven PH (1964) Butterflies and plants: a study in coevolution. Evolution 18: 586–608.
|
[34] | Thompson JN (1994) The coevolutionary process. University of Chicago Press Books 1994.
|
[35] | Fryxell KJ (1996) The coevolution of gene family trees. Trends Genet 12: 364–369.
|
[36] | Pazos F, Valencia A (2008) Protein co-evolution, co-adaptation and interactions. EMBO J 27: 2648–2655.
|
[37] | Clark NL, Aquadro CF (2010) A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins. Mol Biol Evol 27: 1152–1161.
|
[38] | de Juan D, Pazos F, Valencia A (2013) Emerging methods in protein co-evolution. Nat Rev Genet 14: 249–261.
|
[39] | Haag ES, Wang S, Kimble J (2002) Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2. Curr Biol 12: 2035–2041.
|
[40] | Zamir L, Zaretsky M, Fridman Y, Ner-Gaon H, Rubin E, et al. (2012) Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility. Proc Natl Acad Sci U S A 109: E406–E414.
|
[41] | Sandler I, Abu-Qarn M, Aharoni A (2013) Protein co-evolution: how do we combine bioinformatics and experimental approaches? Mol BioSyst 9: 175–181.
|
[42] | Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
|
[43] | Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696–704.
|
[44] | Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE (2000) Co-evolution of proteins with their interaction partners. J Mol Biol 299: 283–293.
|
[45] | Smouse PE, Long J C, Sokal RR (1986) Multiple regression and correlation extensions of the mantel test of matrix correspondence. Syst Zool 35: 627–632.
|
[46] | Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725–736.
|
[47] | Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586–1591.
|
[48] | Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19: 908–917.
|
[49] | Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27: 343–350.
|
[50] | Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915–10919.
|
[51] | Fares MA, Travers SAA (2006) A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics 173: 9–23.
|
[52] | Pazos F, Ranea JA, Juan D, Sternberg MJ (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol 352: 1002–1015.
|
[53] | Weigel D, Alvarez J, Smyth D R, Yanofsky MF, Meyerowitz EM (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69: 843–859.
|
[54] | Winter KU, Weiser C, Kaufmann K, Bohne A, Kirchner C, et al. (2002) Evolution of class B floral homeotic proteins: obligate heterodimerization originated from homodimerization. Mol Biol Evol 19: 587–596.
|
[55] | Lenser T, Theissen G, Dittrich P (2009) Developmental robustness by obligate interaction of class B floral homeotic genes and proteins. PLOS Comput Biol 5: e1000264.
|
[56] | Jelinska C, Conroy MJ, Craven CJ, Hounslow AM, Bullough PA, et al. (2005) Obligate heterodimerization of the archaeal Alba2 protein with Alba1 provides a mechanism for control of DNA packaging. Structure 13: 963–971.
|
[57] | Airoldi CA, Davies B (2012) Gene duplication and the evolution of plant MADS-box transcription factors. J Genet Genomics 39: 157–165.
|
[58] | Clark NL, Gasper J, Sekino M, Springer SA, Aquadro CF, et al. (2009) Coevolution of interacting fertilization proteins. PLOS Genet 5: e1000570.
|
[59] | Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296: 750–752.
|
[60] | Fraser HB, Hirsh AE, Wall DP, Eisen MB (2004) Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A 101: 9033–9038.
|
[61] | Rodionov A, Bezginov A, Rose J, Tillier ER (2011) A new, fast algorithm for detecting protein coevolution using maximum compatible cliques. Algorithms Mol Biol 6: 17.
|
[62] | Fraser HB, Wall DP, Hirsh AE (2003) A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 3: 11.
|
[63] | Saeed R, Deane CM (2006) Protein protein interactions, evolutionary rate, abundance and age. BMC Bioinformatics 7: 128.
|
[64] | Burton RS, Rawson PD, Edmands S (1999) Genetic architecture of physiological phenotypes: empirical evidence for coadapted gene complexes. Amer Zool 39: 451–462.
|