| [1] | Glickman MH, Ciechanover A (2002) The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev 82: 373–428.
|
| [2] | Kerscher O, Felberbaum R, Hochstrasser M (2006) Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol 22: 159–180.
|
| [3] | Chen ZJ, Sun LJ (2009) Nonproteolytic functions of ubiquitin in cell signaling. Mol Cell 33: 275–286.
|
| [4] | Komander D (2009) The emerging complexity of protein ubiquitination. Biochem Soc Trans 37: 937–953.
|
| [5] | Schwartz AL, Ciechanover A (2009) Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology. Annu Rev Pharmacol Toxicol 49: 73–96.
|
| [6] | Behrends C, Harper JW (2011) Constructing and decoding unconventional ubiquitin chains. Nat Struct Mol Biol 18: 520–528.
|
| [7] | Marín I, Ferrús A (2002) Comparative genomics of the RBR family, including the Parkinson’s disease-related gene parkin and the genes of the ariadne subfamily. Mol Biol Evol 19: 2039–2050.
|
| [8] | Marín I, Lucas JI, Gradilla AC, Ferrús A (2004) Parkin and relatives: the RBR family of ubiquitin ligases. Physiol Genomics 17: 253–263.
|
| [9] | Lucas JI, Arnau V, Marín I (2006) Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism. J Mol Biol 357: 9–17.
|
| [10] | Marín I (2009) RBR ubiquitin ligases: Diversification and streamlining in animal lineages. J Mol Evol 69: 54–64.
|
| [11] | Marín I (2010) Diversification and specialization of plant RBR ubiquitin ligases. PLoS One 5: e11579.
|
| [12] | Marín I (2012) Origin and diversification of TRIM ubiquitin ligases. PLoS One, in press.
|
| [13] | Marín I (2009) Diversification of the cullin family. BMC Evol Biol 9: 267.
|
| [14] | Marín I (2010) Ancient origin of animal U-box ubiquitin ligases. BMC Evol Biol 10: 331.
|
| [15] | Marín I (2010) Animal HECT ubiquitin ligases: evolution and functional implications. BMC Evol Biol 10: 56.
|
| [16] | Rotin D, Kumar S (2009) Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol 10: 398–409.
|
| [17] | Dastur A, Beaudenon S, Kelley M, Krug RM, Huibregtse JM (2006) Herc5, an interferon-induced HECT E3 enzyme, is required for conjugation of ISG15 in human cells. J Biol Chem 281: 4334–4338.
|
| [18] | Wong JJ, Pung YF, Sze NS, Chin KC (2006) HERC5 is an IFN-induced HECT-type E3 protein ligase that mediates type I IFN-induced ISGylation of protein targets. Proc Natl Acad Sci U S A 103: 10735–10740.
|
| [19] | Oudshoorn D, van Boheemen S, Sánchez-Aparicio MT, Rajsbaum R, García-Sastre A, et al. (2012) HERC6 is the main E3 ligase for global ISG15 conjugation in mouse cells. PLoS One 7: e29870.
|
| [20] | Scheffner M, Staub O (2007) HECT E3s and human disease. BMC Biochem 8: S6.
|
| [21] | Bernassola F, Karin M, Ciechanover A, Melino G (2008) The HECT family of E3 ubiquitin ligases: multiple players in cancer development. Cancer Cell 14: 10–21.
|
| [22] | Matentzoglu K, Scheffner M (2008) Ubiquitin ligase E6-AP and its role in human disease. Biochem Soc Trans 36: 797–801.
|
| [23] | Chen C, Matesic LE (2007) The Nedd4-like family of E3 ubiquitin ligases and cancer. Cancer Metastasis Rev 26: 587–604.
|
| [24] | Downes BP, Stupar RM, Gingerich DJ, Vierstra RD (2003) The HECT ubiquitin-protein ligase (UPL) family in Arabidopsis: UPL3 has a specific role in trichome development. Plant J 35: 729–742.
|
| [25] | El Refy A, Perazza D, Zekraoui L, Valay JG, Bechtold N, et al. (2003) The Arabidopsis KAKTUS gene encodes a HECT protein and controls the number of endoreduplication cycles. Mol Genet Genomics 270: 403–414.
|
| [26] | Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I (2013) A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages. Genome Biol Evol 5: 833–847.
|
| [27] | Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, et al. (2006) Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 22: 597–602.
|
| [28] | Serrano M, Parra S, Alcaraz LD, Guzmán P (2006) The ATL gene family from Arabidopsis thaliana and Oryza sativa comprises a large number of putative ubiquitin ligases of the RING-H2 type. J Mol Evol 62: 434–45.
|
| [29] | Aguilar-Hernández V, Aguilar-Henonin L, Guzmán P (2011) Diversity in the architecture of ATLs, a family of plant ubiquitin-ligases, leads to recognition and targeting of substrates in different cellular environments. PLoS One 6: e23934.
|
| [30] | Azevedo C, Santos-Rosa MJ, Shirasu K (2001) The U-box protein family in plants. Trends Plant Sci 6: 354–358.
|
| [31] | Zeng LR, Park CH, Venu RC, Gough J, Wang GL (2008) Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins. Mol Plant. 1: 800–815.
|
| [32] | Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD (2002) The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci U S A 99: 11519–11524.
|
| [33] | Kuroda H, Takahashi N, Shimada H, Seki M, Shinozaki K, et al. (2002) Classification and expression analysis of Arabidopsis F-box-containing protein genes. Plant Cell Physiol 43: 1073–1085.
|
| [34] | Thomas JH (2006) Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res 16: 1017–1030.
|
| [35] | Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, et al. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467–1483.
|
| [36] | Yang X, Kalluri UC, Jawdy S, Gunter LE, Yin T, et al. (2008) The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. Plant Physiol 148: 1189–1200.
|
| [37] | Xu G, Ma H, Nei M, Kong H (2009) Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proc Natl Acad Sci U S A 106: 835–40.
|
| [38] | Hua Z, Zou C, Shiu SH, Vierstra RD (2011) Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS One 6: e16219.
|
| [39] | Kong H, Leebens-Mack J, Ni W, dePamphilis CW, Ma H (2004) Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Mol Biol Evol 21: 117–128.
|
| [40] | Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma H, et al. (2007) Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J 50: 873–885.
|
| [41] | Gingerich DJ, Hanada K, Shiu SH, Vierstra RD (2007) Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. Plant Cell 19: 2329–2348.
|
| [42] | Miao Y, Zentgraf U (2010) A HECT E3 ubiquitin ligase negatively regulates Arabidopsis leaf senescence through degradation of the transcription factor WRKY53. Plant J 63: 179–188.
|
| [43] | Craig A, Ewan R, Mesmar J, Gudipati V, Sadanandom A (2009) E3 ubiquitin ligases and plant innate immunity. J Exp Bot 60: 1123–1132.
|
| [44] | Trujillo M, Shirasu K (2010) Ubiquitination in plant immunity. Curr Opin Plant Biol 13: 402–408.
|
| [45] | Dielen AS, Badaoui S, Candresse T, German-Retana S (2010) The ubiquitin/26S proteasome system in plant-pathogen interactions: a never-ending hide-and-seek game. Mol Plant Pathol 11: 293–308.
|
| [46] | Cheng YT, Li X (2012) Ubiquitination in NB-LRR-mediated immunity. Curr Opin Plant Biol 15: 392–399.
|
| [47] | Lyzenga WJ, Stone SL (2012) Abiotic stress tolerance mediated by protein ubiquitination. J Exp Bot 63: 599–616.
|
| [48] | Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.
|
| [49] | Nicholas KB, Nicholas Jr HB (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the author.
|
| [50] | 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.
|
| [51] | Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
|
| [52] | Zdobnov EM, Apweiler R (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847–848.
|
| [53] | Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501–506.
|
