Diversification of the cullin family
© Marín; licensee BioMed Central Ltd. 2009
Received: 13 May 2009
Accepted: 19 November 2009
Published: 19 November 2009
Cullins are proteins involved in ubiquitination through their participation in multisubunit ubiquitin ligase complexes. In this study, I use comparative genomic data to establish the pattern of emergence and diversification of cullins in eukaryotes.
The available data indicate that there were three cullin genes before the unikont/bikont split, which I have called Culα, Culβ and Culγ. Fungal species have quite strictly conserved these three ancestral genes, with only occasional lineage-specific duplications. On the contrary, several additional genes appeared in the animal or plant lineages. For example, the human genes Cul1, Cul2, Cul5, Cul7 and Parc all derive from the ancestral Culα gene. These results, together with the available functional data, suggest that three different types of ubiquitin ligase cullin-containing complexes were already present in early eukaryotic evolution: 1) SCF-like complexes with Culα proteins; 2) Culβ/BTB complexes; and, 3) Complexes containing Culγ and DDB1-like proteins. Complexes containing elongins have arisen more recently and perhaps twice independently in animals and fungi.
Most of the known types of cullin-containing ubiquitin ligase complexes are ancient. The available data suggest that, since the origin of eukaryotes, complex diversity has been mostly generated by combining closely related subunits, while radical innovations, giving rise to novel types of complexes, have been scarce. However, several protist groups not examined so far contain highly divergent cullins, indicating that additional types of complexes may exist.
Ubiquitination is a critical process in all eukaryotic organisms. It is involved in several essential functions, from the regulation of protein levels to roles in cellular signaling, DNA repair, endocytosis or gene expression regulation [1–4]. Ubiquitin ligases (E3s) are basic components of the ubiquitination system. They are a numerous and highly diverse group of enzymes able to transfer ubiquitin to the target proteins . It has been observed that many E3s are single proteins. However, in other cases the ubiquitin ligase function is performed by multiprotein complexes. Particularly significant are cullin-RING ubiquitin ligases (CRLs), a diverse group of E3 complexes characterized by containing both a cullin family protein and a RING finger-containing protein. The roles of the cullin protein in this type of complex are quite well understood. Structural data indicate that cullins act as backbones that facilitate ubiquitination by correctly positioning both the RING finger-containing protein, that recruits the ubiquitin-conjugating enzyme (E2), and another protein present in the CRL complex, the substrate receptor, which confers substrate specificity. The CRL complexes also often contain one or more adaptor proteins, which at the same time bind the cullin and recruit the substrate receptor [5, 6].
CRLs are the most abundant E3s. Their diversity is due to the fact that many alternative complexes can be generated in a combinatorial way: multiple related proteins may substitute each other to form similar but functionally distinct complexes. The number of CRLs may be very large: in all eukaryotic species analyzed in detail so far there are several cullins, related RING finger-containing proteins, several adaptors and, most especially, many alternative substrate receptors (e. g. potentially, there may be several hundreds in mammals) that participate in CRLs. Fortunately, and in spite of this extensive variability, analyses in multiple species has allowed to classify all complexes known so far into a few main CRL classes: 1) the Cullin/RING/Skp/F-box CRLs (historically known as SCF complexes, and to which I will refer generically as F-box CRLs) that contain proteins with F boxes as substrate receptors and Skp1 or related proteins as adaptors; 2) the Cullin/RING/BTB CRLs (BTB CRLs), characterized by lacking additional adaptors and containing proteins with BTB domains as substrate receptors, directly bound to the cullins; 3) the Cullin/RING/DDB/DCAFs CRLs (DDB CRLs) that contain proteins related to mammalian DDB1 as adaptors and often proteins with WD40 domains as substrate receptors; and, 4) Cullin/RING/Elongins/BC-box CRLs (BC-box CRLs), which contain one or two elongin proteins as adaptors and BC-box/SOCS-box containing proteins as substrate receptors (see reviews [5–9]).
It is known that CRLs regulate multiple cellular and developmental pathways in animals, fungi and plants, and certainly that may hold true for all free living eukaryotes (see e. g. refs. [5, 6]). In addition of the intrinsic importance of cullins as critical players in ubiquitination control, they have recently received additional attention due to implication of mutations in cullin-encoding genes in several human diseases [10–13]. It is thus surprising that large-scale studies of the CRL complexes from a comparative point of view have not been hitherto performed. For example, no systematic efforts to determine the evolution of cullin proteins in the eukaryotes as a whole have been attempted. There were only some studies in which a few sequences were examined from an evolutionary point of view [14–18]. This has caused significant problems. A typical one is the assignation of the same names to genes in different species just because the proteins that they encode belong to complexes with similar units (for example, similar adaptors and substrate receptors), without any data actually supporting that those genes are orthologous. In addition, in some cases genes were named identically while being described independently in different species -- typically the names included the term cullin plus a consecutive number -- without considering at all their relationships. Thus, the current literature contains a significant degree of uncertainty about the similarities and differences of cullins and CRL complexes in different species, which may lead to inappropriate translations of the functional results obtained in one species to the rest. As a step to characterize the evolution of CRL complexes, I describe here the first comprehensive analysis of the evolution of cullin proteins. The results obtained in this study confirm several well-established ideas in the field, but also open some novel perspectives.
Generation of a database of cullin proteins
The protein sequences corresponding to the most conserved region of twelve cullin proteins were used in TblastN searches to find all members of this family present at the nr, est, gss, htgs or wgs databases of the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/). These sequences were selected both to cover all the variation detected in previous analyses of cullin proteins and also to specifically check for all members of potential new families, most especially in protozoans. The selected genes derived from Homo sapiens (Cul3 and Cul7 proteins), Drosophila melanogaster (CG11261), Caenorhabditis elegans (Cul4), Saccharomyces cerevisiae (Cul8), Debaryomyces hansenii (Accession number CR382135.2), Cyanidioschyzon merolae (Acc. No. AP006495.1), Plasmodium falciparum (Acc. No. XM_961187.1), Trypanosoma brucei (Acc. Nos. XM_842334.1, XM_839532.1 and XM_838630.1) and Leishmania major (Acc. No. XM_001684442.1). The conserved region of the proteins used in these searches was homologous to amino acids 420 - 776 in human Cullin1. Once excluded partial sequences (< 300 amino acids), duplicates or nearly identical sequences (≥ 99% identity) and highly divergent sequences that could not be reliably aligned along the whole length of the selected region, I generated a database containing 490 sequences (available as Additional File 1). The cullin domain-containing APC2 proteins will not be considered here, given that their similarity with canonical cullins was too low. The rest of cullins, including the highly divergent cullin domain-containing CUL7 and PARC proteins of vertebrates, which were indeed easily detected and aligned, were all included in this study.
Phylogenetic and structural analyses
Protein sequences were aligned using ClustalX 2.07  and manually corrected using GeneDoc . Multiple dendrograms (see Results) were then built using data extracted from that primary alignment. Three different procedures to generate those dendrograms were used, namely Neighbor joining (NJ), Maximum parsimony (MP) and Maximum likelihood (ML). The NJ tree was obtained using the routine in MEGA 4  MP analyses were performed using PAUP* beta 10 version  and ML reconstructions were established using PhyML 2.4.4 . For NJ, sites with gaps were treated with the pairwise deletion option (as recommended by ) and Kimura's correction implemented. Parameters for MP were as follows: 1) all sites included, gaps treated as unknown characters; 2) randomly generated trees used as seeds; 3) maximum number of trees saved equal to 100; and, 4) heuristic search using the subtree pruning-regrafting algorithm. Finally, for ML analyses, the BioNJ tree was used to start the iterative searches and the Blosum62 matrix was chosen to model amino acidic substitutions. Gaps are also treated by PhyML as unknown characters. Reliability of the topologies was tested in all cases by bootstrap analyses. 1000 bootstrap replicates were performed for the NJ and MP analyses and 200 for the ML analyses, which are much more computer intensive. Dendrograms were drawn using the tree editor of MEGA 4. Domains in cullin proteins were characterized using InterProScan .
Characterization of the types of cullins present in animals, plants and fungi
The sequences of cullin proteins are very diverse, so general trees containing all the sequences found in the TblastN searches failed to unravel the relationships among the sequences of distant species (as an example, see the NJ tree for the 490 sequences in Additional File 2). In addition, structural analyses failed to detect significant features that might be used to establish relationships among proteins. InterProScan analyses showed that all cullins have a variable N-terminal end, which generally is detected as containing the InterPro domain IPR016159 ("Cullin repeat"), a central, highly conserved region that contains the InterPro domain IPR016158 ("Cullin homology domain") and a C terminus, also highly conserved, that includes the Pfam PF10557 domain ("Cullin_Nedd8 domain"), required for cullin neddylation, an essential step in CRL activity regulation (reviewed in refs. [6, 8, 9]). The two last domains were the ones included in the sequences that I examined. The only exceptions observed after sampling multiple representative sequences belonging to all the main groups of cullins detected in this study, were on one hand some Plasmodium proteins (e. g. Plasmodium falciparum Acc. No. NC_004327.1), which apparently lack the Cullin_Nedd8 domain and, on the other hand, the complex Cul7 and Parc proteins, which are encoded by genes derived from gene fusions, as we already described before [26, 27].
Results in Figure 1 are very well supported and confirm the accepted classification of animal cullins into six main orthology groups, CUL1, CUL2, CUL3; CUL4, CUL5 and CUL7/PARC which respectively include the human genes Cul1, Cul2, Cul3, Cul4A and Cul4B (both in the CUL4 group), Cul5, Cul7 and Parc (the last two in the CUL7/PARC group). For five of those groups (CUL1 - CUL5), I found genes in the placozoan Trichoplax adhaerens and the cnidarian Nematostella vectensis, indicating that they originated before the split of the different animal lineages. On the contrary, genes in the CUL7/PARC group are restricted to chordates and some species of the Drosophila genus contain an additional gene that cannot be ascribed to any of the main classes (forming the CUL-Dros group in Figure 1). We can assume this is a recent fly-specific duplicate that diverged extensively from the rest of cullins in a short period of time.
To interpret the evolutionary history of fungal cullins is more difficult. Figure 2 shows the main groups detected for which there is bootstrap support. It is very significant that, except for some species-specific duplicates, all fungi have three cullin genes. Thus, the simplest hypothesis to explain the results shown in Figure 2 is that three genes existed before the ascomycetes/basidiomycetes split. These three genes would correspond respectively to the CDC53, CUL3 and CUL8/RTT101 genes of Saccharomyces cerevisiae or, also respectively, to the cul1, cul3 and cul4 genes of Schizosaccharomyces pombe. The problem with this hypothesis is the absence of a strong support for the putative Cul3 and Cul4/Cul8 branches (see Figure 2). Especially troublesome is that the CUL8/RTT101 genes of saccharomycotina species are very different from the cul4-like genes of the rest of ascomycetes and basidiomycetes (see also Figure 2). This can be explained in two different ways. One option is that CUL8/RTT101 genes in saccharomycotina are indeed cul4-like genes that have suffered an acceleration of their evolutionary rates which makes difficult to determine their precise phylogenetic position. A second, albeit less parsimonious option, is that saccharomycotina species have lost their ancestral cul4-like gene and in parallel an additional cullin gene arose by duplication, giving rise to the CUL8/RTT101 gene. In any case, no matter which of those two possible explanations is true, it should be possible to determine with precision the phylogenetic relationships of all the rest of fungal cullin genes, once saccharomycotina species are eliminated. This is shown in Figure 3, in which it is clear that the cullins in the rest of fungi all belong to one of the three groups, Cul1, Cul3 or Cul4. The conclusion is that three genes existed when fungi emerged.
Figure 4 shows the result for the set of cullin sequences obtained from bikont species. Interestingly, there are three main groups, highly supported by bootstrap analyses, which include sequences from viridiplantae (plants, green algae) and stramenopiles. Multiple, very similar paralogous genes, evidently associated to their well-known genome duplications, appear in most plant species (see details in Additional file 5). For example, one of the three main groups contain three Arabidopsis thaliana genes (known as Cul1, Cul2 and Cul2-like/Cul2b, this last one a likely pseudogen), a second group includes two genes (named Cul3a and Cul3b) and the third just a single gene, Cul4. This agrees with previous results ([16–18]; additionally, these authors described small cullin-like proteins which did not align along the whole length of the region that I considered in this study and therefore were discarded). The fact that in plants, stramenopiles and fungi the basic, ancestral number of cullin genes is three suggests that these genes may, in origin, be the same. This possibility will be explored in the next section.
Reconciling the phylogenetic trees of animals, fungi and plants
The results shown in the previous section confirm or clarify several relevant aspects of the origin and evolution of cullins, but on the other hand open new significant questions. Of particular interest is to correlate the known biochemical roles of the different cullins (e. g. in which type of CRL they participate) with their diversification. A related point is to establish when the different types of cullins emerged. Data presented in the previous section are compatible with the presence of at least three cullin genes before the unikont/bikont split, followed by lineage-specific duplications. However, more complex alternatives, with some genes disappearing and others emerging in multiple lineages can also be put forward to explain those results. Therefore, I decided to further explore the data in order to determine the most likely scenario for the early evolution of cullins.
Types of cullin complexes characterized so far in different organisms.
Cul7 - Skp1 - F-box proteins 
Cul3 - BTB 
Cul3 - Elongin C - Elongin A (BC box) ?? 
Cul8/Rtt101-Mms1 (DDB-like) 
Cul1 - Skp - F-box proteins 
Cul3 - BTB ( S. pombe ) 
Cul4 - Rik 1 (DDB-like) 
Cul1 - Ask (Skp1-like) - F-box 
Culα- Skp1 - F-box CRL
Culβ- BTB CRL
Culγ - DDB1 CRL
The results obtained are compatible with the presence of three cullin genes (which I have named Culα, Culβ and Culγ) in early eukaryotic evolution. This hypothesis is supported by the independent results in the different groups on which I have focused this study (mainly animals, fungi and plants; Figures 1, 2, 3 and 4), and especially by the combined results when all the sequences in animals and plants and a selected group of slowly evolving sequences from fungi are analyzed together (Figure 5) and fit well with the available functional data (Table 1). We can thus conclude that, in spite of a substantial sequence divergence that complicates the analyses, orthology relationships can be established among cullins of distantly related eukaryotes. In general, the associations found agree well with previous results. For example, the close relationships among Cul3 and Cul4 genes in animals, fungi and plants were observed before [17, 18]. However, my results also provide some additional interesting information which contributes to understand the relationships among all cullins. For example, it can be deduced from the results shown in Figures 1 and 5 that the animal genes Cul1, Cul2, Cul5, Cul7, Parc and Cul-Dros all derive from the ancestral Culα gene. These means that they are all equally related to the Cul1/Cdc53 genes in yeasts and to the Cul1/Cul2 genes in plants, a result that is very significant if we want to compare functional results in different model species. These results also demonstrate that it is inappropriate to use the name Cul2 for plant genes which in fact are plant-specific duplicates, totally unrelated to animal Cul2 genes. In fact, previous analyses had failed to properly situate the plant Cul1/Cul2 branch [17, 18], which I have shown here to clearly correspond to the Culα plant sequences (Figure 4). A final, logical conclusion of the results presented here is that to generate a revised cullin nomenclature based on evolutionary relationships would be advisable. A logical step would be to include in the name of the genes an indication to which group (α, β or γ) they belong.
Once established the most likely orthology relationships among genes, it is possible to evaluate when each type of CRL complex may have arisen. We may deduce in which type of complexes the three different ancestral cullins were involved, by considering what is currently known in model species (Table 1). The most parsimonious conclusion is that each type of cullin was already involved in a different type of complex. Therefore, it can be hypothesized that there were three types of cullin complexes in early eukaryotes: F-box CRLs, BTB CRLs and DDB CRLs (see data in Table 1). The rest of complexes must have arisen more recently. Thus, both the animal Cul2/Elongin and Cul5/Elongin complexes (Table 1) must be animal-specific, considering the relatively recent emergence of those two genes, already described. Finally, the description of a Cul3/Elongin complex in the yeast Saccharomyces cerevisiae (Table 1) is incongruent. The fact that no other Cul3 protein has ever been found to interact with elongins and that the elongin-containing complexes in animals only involve animal-specific cullins, as I just mentioned, suggest that all complexes that include adaptors with BC boxes (VHL, SOCS proteins, Elongin A, etc.; see details in the references listed in Table 1) emerged relatively recently. The presence of those complexes in both animals and (if confirmed) in Saccharomyces must therefore be due to parallel evolution: the same novel interaction between cullins and BC box-containing proteins emerged twice independently. This conclusion would be falsified only if additional Cul3/Elongin A complexes in animals or plants are found. On the other hand, so far no Cul3/BTB CRL complex has been described in Saccharomyces. However, the finding of such complexes in plants, animals and even other fungi strongly suggest that they must exist also in budding yeast species. Perhaps, as I already suggested above, this means that Cul3 in Saccharomyces participates in two different complexes, one of them involving elongins and a second one involving BTB-containing adaptors.
A final consideration is that the discovery of multiple, highly divergent multiple cullin genes in some protozoans, and especially species of the Alveolata and Excavata groups (Figure 3) suggests that the spectrum of possible CRL complexes in eukaryotes may be much wider than the scientific community has so far established. At a more local level, the substantial diversification of the Cul4 sequences in some fungi, especially the saccharomycotina (Figure 2), may also be an indication of them having acquired peculiar functional features. These possibilities may be experimentally explored in the near future. Finally, it is also interesting to point out that APC2 genes, not considered here given its low degree of similarity, may all derive from a fourth gene with a cullin domain that also emerged before the unikont/bikont split [57–60].
The origin of most of the known types of CRLs is ancient. The current diversity of CRL complexes in animals, plants and fungi is mostly explained by the emergence of different combinations of related proteins to give rise to multiple similar complexes. So far, a single type of complex is known that emerged since the unikont/bikont split, and perhaps twice independently in animals and fungi. However, the characterization of CRL complexes in additional protists (e. g. alveolata, excavata) may lead to the discovery of additional novel types of complexes of recent origin.
This project was supported by grant BIO2008-05067 (Programa Nacional de Biotecnología; Ministerio de Ciencia e Innovación. Spain).
- Glickman MH, Ciechanover A: The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev. 2002, 82: 373-428.View ArticlePubMedGoogle Scholar
- Kerscher O, Felberbaum R, Hochstrasser M: Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol. 2006, 22: 159-180. 10.1146/annurev.cellbio.22.010605.093503.View ArticlePubMedGoogle Scholar
- Mukhopadhyay D, Riezman H: Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science. 2007, 315: 201-205. 10.1126/science.1127085.View ArticlePubMedGoogle Scholar
- Schwartz AL, Ciechanover A: Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology. Annu Rev Pharmacol Toxicol. 2009, 49: 73-96. 10.1146/annurev.pharmtox.051208.165340.View ArticlePubMedGoogle Scholar
- Willems AR, Schwab M, Tyers M: A hitchhiker's guide to the cullin ubiquitin ligases: SCF and its kin. Biochim Biophys Acta. 2004, 1695: 133-170. 10.1016/j.bbamcr.2004.09.027.View ArticlePubMedGoogle Scholar
- Petroski MD, Deshaies RJ: Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol. 2005, 6: 9-20. 10.1038/nrm1547.View ArticlePubMedGoogle Scholar
- Lee J, Zhou P: DCAFs, the missing link of the CUL4-DDB1 ubiquitin ligase. Mol Cell. 2007, 26: 775-780. 10.1016/j.molcel.2007.06.001.View ArticlePubMedGoogle Scholar
- Hotton SK, Callis J: Regulation of cullin RING ligases. Annu Rev Plant Biol. 2008, 59: 467-489. 10.1146/annurev.arplant.58.032806.104011.View ArticlePubMedGoogle Scholar
- Bosu DR, Kipreos ET: Cullin-RING ubiquitin ligases: global regulation and activation cycles. Cell Div. 2008, 3: 7-10.1186/1747-1028-3-7.PubMed CentralView ArticlePubMedGoogle Scholar
- Huber C, Dias-Santagata D, Glaser A, O'Sullivan J, Brauner R, Wu K, Xu X, Pearce K, Wang R, Uzielli ML, Dagoneau N, Chemaitilly W, Superti-Furga A, Dos Santos H, Mégarbané A, Morin G, Gillessen-Kaesbach G, Hennekam R, Burgt Van der I, Black GC, Clayton PE, Read A, Le Merrer M, Scambler PJ, Munnich A, Pan ZQ, Winter R, Cormier-Daire V: Identification of mutations in CUL7 in 3-M syndrome. Nat Genet. 2005, 37: 1119-1124. 10.1038/ng1628.View ArticlePubMedGoogle Scholar
- Maksimova N, Hara K, Miyashia A, Nikolaeva I, Shiga A, Nogovicina A, Sukhomyasova A, Argunov V, Shvedova A, Ikeuchi T, Nishizawa M, Kuwano R, Onodera O: Clinical, molecular and histopathological features of short stature syndrome with novel CUL7 mutation in Yakuts: new population isolate in Asia. J Med Genet. 2007, 44: 772-778. 10.1136/jmg.2007.051979.PubMed CentralView ArticlePubMedGoogle Scholar
- Tarpey PS, Raymond FL, O'Meara S, Edkins S, Teague J, Butler A, Dicks E, Stevens C, Tofts C, Avis T, Barthorpe S, Buck G, Cole J, Gray K, Halliday K, Harrison R, Hills K, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Varian J, West S, Widaa S, Mallya U, Moon J, Luo Y, Holder S, Smithson SF, Hurst JA, Clayton-Smith J, Kerr B, Boyle J, Shaw M, Vandeleur L, Rodriguez J, Slaugh R, Easton DF, Wooster R, Bobrow M, Srivastava AK, Stevenson RE, Schwartz CE, Turner G, Gecz J, Futreal PA, Stratton MR, Partington M: Mutations in CUL4B, which encodes a ubiquitin E3 ligase subunit, cause an X-linked mental retardation syndrome associated with aggressive outbursts, seizures, relative macrocephaly, central obesity, hypogonadism, pes cavus, and tremor. Am J Hum Genet. 2007, 80: 345-352. 10.1086/511134.PubMed CentralView ArticlePubMedGoogle Scholar
- Zou Y, Liu Q, Chen B, Zhang X, Guo C, Zhou H, Li J, Gao G, Guo Y, Yan C, Wei J, Shao C, Gong Y: Mutation in CUL4B, which encodes a member of cullin-RING ubiquitin ligase complex, causes X-linked mental retardation. Am J Hum Genet. 2007, 80: 561-566. 10.1086/512489.PubMed CentralView ArticlePubMedGoogle Scholar
- Kipreos ET, Lander LE, Wing JP, He WW, Hedgecock EM: cul-1 is required for cell cycle exit in C. elegans and identifies a novel gene family. Cell. 1996, 85: 829-839. 10.1016/S0092-8674(00)81267-2.View ArticlePubMedGoogle Scholar
- Nayak S, Santiago FE, Jin H, Lin D, Schedl T, Kipreos ET: The Caenorhabditis elegans Skp1-related gene family: diverse functions in cell proliferation, morphogenesis, and meiosis. Curr Biol. 2002, 12: 277-287. 10.1016/S0960-9822(02)00682-6.View ArticlePubMedGoogle Scholar
- Shen WH, Parmentier Y, Hellmann H, Lechner E, Dong A, Masson J, Granier F, Lepiniec L, Estelle M, Genschik P: Null mutation of AtCUL1 causes arrest in early embryogenesis in Arabidopsis. Mol Biol Cell. 2002, 13: 1916-1928. 10.1091/mbc.E02-02-0077.PubMed CentralView ArticlePubMedGoogle Scholar
- Risseeuw EP, Daskalchuk TE, Banks TW, Liu E, Cotelesage J, Hellmann H, Estelle M, Somers DE, Crosby WL: Protein interaction analysis of SCF ubiquitin E3 ligase subunits from Arabidopsis. Plant J. 2003, 34: 753-767. 10.1046/j.1365-313X.2003.01768.x.View ArticlePubMedGoogle Scholar
- Gingerich DJ, Gagne JM, Salter DW, Hellmann H, Estelle M, Ma L, Vierstra RD: Cullins 3a and 3b assemble with members of the broad complex/tramtrack/bric-a-brac (BTB) protein family to form essential ubiquitin-protein ligases (E3s) in Arabidopsis. J Biol Chem. 2005, 280: 18810-18821. 10.1074/jbc.M413247200.View ArticlePubMedGoogle Scholar
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948. 10.1093/bioinformatics/btm404.View ArticlePubMedGoogle Scholar
- Nicholas KB, Nicholas HB: GeneDoc: a tool for editing and annotating multiple sequence alignments. distributed by the authors. 1997, [http://www.nrbsc.org/gfx/genedoc/index.html]Google Scholar
- Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24: 1596-1599. 10.1093/molbev/msm092.View ArticlePubMedGoogle Scholar
- Swofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. 2002, Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
- Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080/10635150390235520.View ArticlePubMedGoogle Scholar
- Dwivedi B, Gadagkar SR: Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol Biol. 2009, 9: 211-10.1186/1471-2148-9-211.PubMed CentralView ArticlePubMedGoogle Scholar
- Zdobnov EM, Apweiler R: InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001, 17: 847-848. 10.1093/bioinformatics/17.9.847.View ArticlePubMedGoogle Scholar
- Marín I, Ferrús A: Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the ariadne subfamily. Mol Biol Evol. 2002, 19: 2039-2050.View ArticlePubMedGoogle Scholar
- Marín I, Lucas JI, Gradilla AC, Ferrús A: Parkin and relatives: the RBR family of ubiquitin ligases. Physiol Genomics. 2004, 17: 253-263. 10.1152/physiolgenomics.00226.2003.View ArticlePubMedGoogle Scholar
- Feldman RM, Correll CC, Kaplan KB, Deshaies RJ: A complex of Cdc4p, Skp1p, and Cdc53p/cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p. Cell. 1997, 91: 221-230. 10.1016/S0092-8674(00)80404-3.View ArticlePubMedGoogle Scholar
- Skowyra D, Craig KL, Tyers M, Elledge SJ, Harper JW: F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex. Cell. 1997, 91: 209-219. 10.1016/S0092-8674(00)80403-1.View ArticlePubMedGoogle Scholar
- Kominami K, Ochotorena I, Toda T: Two F-box/WD-repeat proteins Pop1 and Pop2 form hetero- and homo-complexes together with cullin-1 in the fission yeast SCF (Skp1-Cullin-1-F-box) ubiquitin ligase. Genes Cells. 1998, 3: 721-735. 10.1046/j.1365-2443.1998.00225.x.View ArticlePubMedGoogle Scholar
- Lisztwan J, Marti A, Sutterlüty H, Gstaiger M, Wirbelauer C, Krek W: Association of human CUL-1 and ubiquitin-conjugating enzyme CDC34 with the F-box protein p45(SKP2): evidence for evolutionary conservation in the subunit composition of the CDC34-SCF pathway. EMBO J. 1998, 17: 368-383. 10.1093/emboj/17.2.368.PubMed CentralView ArticlePubMedGoogle Scholar
- Lyapina SA, Correll CC, Kipreos ET, Deshaies RJ: Human CUL1 forms an evolutionarily conserved ubiquitin ligase complex (SCF) with SKP1 and an F-box protein. Proc Natl Acad Sci USA. 1998, 95: 7451-7456. 10.1073/pnas.95.13.7451.PubMed CentralView ArticlePubMedGoogle Scholar
- Gray WM, del Pozo JC, Walker L, Hobbie L, Risseeuw E, Banks T, Crosby WL, Yang M, Ma H, Estelle M: Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana. Genes Dev. 1999, 13: 1678-1691. 10.1101/gad.13.13.1678.PubMed CentralView ArticlePubMedGoogle Scholar
- Dias DC, Dolios G, Wang R, Pan ZQ: CUL7: A DOC domain-containing cullin selectively binds Skp1.Fbx29 to form an SCF-like complex. Proc Natl Acad Sci USA. 2002, 99: 16601-16606. 10.1073/pnas.252646399.PubMed CentralView ArticlePubMedGoogle Scholar
- Furukawa M, He YJ, Borchers C, Xiong Y: Targeting of protein ubiquitination by BTB-Cullin 3-Roc1 ubiquitin ligases. Nat Cell Biol. 2003, 5: 1001-1007. 10.1038/ncb1056.View ArticlePubMedGoogle Scholar
- Geyer R, Wee S, Anderson S, Yates J, Wolf DA: BTB/POZ domain proteins are putative substrate adaptors for cullin 3 ubiquitin ligases. Mol Cell. 2003, 12: 783-790. 10.1016/S1097-2765(03)00341-1.View ArticlePubMedGoogle Scholar
- Weber H, Bernhardt A, Dieterle M, Hano P, Mutlu A, Estelle M, Genschik P, Hellmann H: Arabidopsis AtCUL3a and AtCUL3b form complexes with members of the BTB/POZ-MATH protein family. Plant Physiol. 2005, 137: 83-93. 10.1104/pp.104.052654.PubMed CentralView ArticlePubMedGoogle Scholar
- Dieterle M, Thomann A, Renou JP, Parmentier Y, Cognat V, Lemonnier G, Müller R, Shen WH, Kretsch T, Genschik P: Molecular and functional characterization of Arabidopsis Cullin 3A. Plant J. 2005, 41: 386-399. 10.1111/j.1365-313X.2004.02302.x.View ArticlePubMedGoogle Scholar
- Gingerich DJ, Gagne JM, Salter DW, Hellmann H, Estelle M, Ma L, Vierstra RD: Cullins 3a and 3b assemble with members of the broad complex/tramtrack/bric-a-brac (BTB) protein family to form essential ubiquitin-protein ligases (E3s) in Arabidopsis. J Biol Chem. 2005, 280: 18810-18821. 10.1074/jbc.M413247200.View ArticlePubMedGoogle Scholar
- Figueroa P, Gusmaroli G, Serino G, Habashi J, Ma L, Shen Y, Feng S, Bostick M, Callis J, Hellmann H, Deng XW: Arabidopsis has two redundant Cullin3 proteins that are essential for embryo development and that interact with RBX1 and BTB proteins to form multisubunit E3 ubiquitin ligase complexes in vivo. Plant Cell. 2005, 17: 1180-1195. 10.1105/tpc.105.031989.PubMed CentralView ArticlePubMedGoogle Scholar
- Shiyanov P, Nag A, Raychaudhuri P: Cullin 4A associates with the UV-damaged DNA-binding protein DDB. J Biol Chem. 1999, 274: 35309-35312. 10.1074/jbc.274.50.35309.View ArticlePubMedGoogle Scholar
- Jia S, Kobayashi R, Grewal SI: Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol. 2005, 7: 1007-1013. 10.1038/ncb1300.View ArticlePubMedGoogle Scholar
- Bernhardt A, Lechner E, Hano P, Schade V, Dieterle M, Anders M, Dubin MJ, Benvenuto G, Bowler C, Genschik P, Hellmann H: CUL4 associates with DDB1 and DET1 and its downregulation affects diverse aspects of development in Arabidopsis thaliana. Plant J. 2006, 47: 591-603. 10.1111/j.1365-313X.2006.02810.x.View ArticlePubMedGoogle Scholar
- Chen H, Shen Y, Tang X, Yu L, Wang J, Guo L, Zhang Y, Zhang H, Feng S, Strickland E, Zheng N, Deng XW: Arabidopsis CULLIN4 forms an E3 ubiquitin ligase with RBX1 and the CDD complex in mediating light control of development. Plant Cell. 2006, 18: 1991-2004. 10.1105/tpc.106.043224.PubMed CentralView ArticlePubMedGoogle Scholar
- Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N: Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature. 2006, 443: 590-593.PubMedGoogle Scholar
- He YJ, McCall CM, Hu J, Zeng Y, Xiong Y: DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4-ROC1 ubiquitin ligases. Genes Dev. 2006, 20: 2949-2954. 10.1101/gad.1483206.PubMed CentralView ArticlePubMedGoogle Scholar
- Higa LA, Wu M, Ye T, Kobayashi R, Sun H, Zhang H: CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol. 2006, 8: 1277-1283. 10.1038/ncb1490.View ArticlePubMedGoogle Scholar
- Jin J, Arias EE, Chen J, Harper JW, Walter JC: A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1. Mol Cell. 2006, 23: 709-721. 10.1016/j.molcel.2006.08.010.View ArticlePubMedGoogle Scholar
- Zaidi IW, Rabut G, Poveda A, Scheel H, Malmström J, Ulrich H, Hofmann K, Pasero P, Peter M, Luke B: Rtt101 and Mms1 in budding yeast form a CUL4(DDB1)-like ubiquitin ligase that promotes replication through damaged DNA. EMBO Rep. 2008, 9: 1034-1040. 10.1038/embor.2008.155.PubMed CentralView ArticlePubMedGoogle Scholar
- Guerrero-Santoro J, Kapetanaki MG, Hsieh CL, Gorbachinsky I, Levine AS, Rapiæ-Otrin V: The cullin 4B-based UV-damaged DNA-binding protein ligase binds to UV-damaged chromatin and ubiquitinates histone H2A. Cancer Res. 2008, 68: 5014-5022. 10.1158/0008-5472.CAN-07-6162.View ArticlePubMedGoogle Scholar
- Pause A, Lee S, Worrell RA, Chen DY, Burgess WH, Linehan WM, Klausner RD: The von Hippel-Lindau tumor-suppressor gene product forms a stable complex with human CUL-2, a member of the Cdc53 family of proteins. Proc Natl Acad Sci USA. 1997, 94: 2156-2161. 10.1073/pnas.94.6.2156.PubMed CentralView ArticlePubMedGoogle Scholar
- Kamura T, Koepp DM, Conrad MN, Skowyra D, Moreland RJ, Iliopoulos O, Lane WS, Kaelin WG, Elledge SJ, Conaway RC, Harper JW, Conaway JW: Rbx1, a component of the VHL tumor suppressor complex and SCF ubiquitin ligase. Science. 1999, 284: 657-661. 10.1126/science.284.5414.657.View ArticlePubMedGoogle Scholar
- Kamura T, Burian D, Yan Q, Schmidt SL, Lane WS, Querido E, Branton PE, Shilatifard A, Conaway RC, Conaway JW: Muf1, a novel Elongin BC-interacting leucine-rich repeat protein that can assemble with Cul5 and Rbx1 to reconstitute a ubiquitin ligase. J Biol Chem. 2001, 276: 29748-29753. 10.1074/jbc.M103093200.View ArticlePubMedGoogle Scholar
- Kamura T, Maenaka K, Kotoshiba S, Matsumoto M, Kohda D, Conaway RC, Conaway JW, Nakayama KI: VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases. Genes Dev. 2004, 18: 3055-3065. 10.1101/gad.1252404.PubMed CentralView ArticlePubMedGoogle Scholar
- Yasukawa T, Kamura T, Kitajima S, Conaway RC, Conaway JW, Aso T: Mammalian Elongin A complex mediates DNA-damage-induced ubiquitylation and degradation of Rpb1. EMBO J. 2008, 27: 3256-3266. 10.1038/emboj.2008.249.PubMed CentralView ArticlePubMedGoogle Scholar
- Ribar B, Prakash L, Prakash S: ELA1 and CUL3 are required along with ELC1 for RNA polymerase II polyubiquitylation and degradation in DNA-damaged yeast cells. Mol Cell Biol. 2007, 27: 3211-3216. 10.1128/MCB.00091-07.PubMed CentralView ArticlePubMedGoogle Scholar
- Zachariae W, Shevchenko A, Andrews PD, Ciosk R, Galova M, Stark MJR, Mann M, Nasmyth K: Mass spectrometric analysis of the anaphase-promoting complex from yeast: Identification of a subunit related to cullins. Science. 1998, 279: 1216-1219. 10.1126/science.279.5354.1216.View ArticlePubMedGoogle Scholar
- Yu H, Peters JM, King RW, Page AM, Hieter P, Kirschner MW: Identification of a cullin homology region in a subunit of the anaphase-promoting complex. Science. 1998, 279: 1219-1222. 10.1126/science.279.5354.1219.View ArticlePubMedGoogle Scholar
- Capron A, Ökrész L, Genschik P: First glance at the plant APC/C, a highly conserved ubiquitin-protein ligase. Trends Plant Sci. 2003, 8: 83-89. 10.1016/S1360-1385(02)00028-6.View ArticlePubMedGoogle Scholar
- Capron A, Serralbo O, Fülöp K, Frugier F, Parmentier Y, Dong A, Lecureuil A, Guerche P, Kondorosi E, Scheres B, Genschik P: The Arabidopsis anaphase-promoting complex or cyclosome: molecular and genetic characterization of the APC2 subunit. Plant Cell. 2003, 15: 2370-2382. 10.1105/tpc.013847.PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.