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The intracellular region of Notch ligands: does the tail make the difference?

Biology Direct volume 2, Article number: 19 (2007) Cite this article

Abstract

Abstract

The cytoplasmic tail of Notch ligands drives endocytosis, mediates association with proteins implicated in the organization of cell-cell junctions and, through regulated intra-membrane proteolysis, is released from the membrane as a signaling fragment. We survey these findings and discuss the role of Notch ligands intracellular region in bidirectional signaling and possibly in signal modulation in mammals.

Reviewers

This article was reviewed by Frank Eisenhaber, L Aravind, and Eugene V. Koonin.

Background

Notch-mediated signal transduction controls cell fate and is a key process in tissue patterning and morphogenesis [1]. Both receptors and ligands are membrane-bound proteins, the first ones being non-covalent, membrane-spanning heterodimers, the latters single pass, type I membrane proteins [1]. In response to ligand binding, the membrane-spanning subunit of the receptor (NTM) is cleaved by an extracellular ADAM-type (A D isintegrin A nd M etalloprotease) proteinase. This cleavage facilitates a further cleavage of NTM, within the trans-membrane region, carried out by the presenilin/γ-secretase protease and releases the intracellular domain (ICN) from the membrane [2]. This series of controlled proteolytic events is referred to as "regulated intra-membrane proteolysis" or RIP. Once translocated into the nucleus, the ICN interacts with nuclear factors that activate transcription, the main target being a transcription factor (CSL) called C BF1/RBP in mammals, S uppressor of Hairless in Drosophila, and L AG-1 in C. elegans.

The core mechanism of the Notch pathway can be thus viewed as the release of a transcriptional regulator from the membrane, triggered by ligand/receptor interactions and controlled at various levels. The established role of Notch signaling in angiogenesis [3], in T cell development [4], in the maintenance of stem cells [5], in genetic disorders [6] as well as in cancer [7, 8] has been extensively reviewed. The Notch pathway has been identified as a new potential target for cancer therapy [9, 10] and might also be involved in cognitive disorders [11]. Other aspects of Notch signaling, such as its regulation by endocytic processes [12] and receptor glycosylation [13], and the cross-talk between Notch and other signaling pathways [14, 15] have also been reviewed.

Here, we focus on a relatively recent and potentially novel aspect of Notch signaling in mammals: the role of the intracellular region of the membrane-spanning ligands in the interaction with membrane-associated proteins, in the endocytic processes that control receptor/ligand interactions, and as membrane-tethered signaling fragments.

Does the tail make the difference?

All Notch ligands share a similar architecture (Figure 1): a poorly characterized N-terminal region required for receptor binding, a Delta/Serrate/Lag-2 (DSL) domain, a variable number of EGF-like repeats, a trans-membrane segment, and a relatively short (~100–150 amino acids) cytoplasmic tail [16]. Traditionally, ligands are classified in two distinct families: homologues of Drosophila Delta protein (Delta-1, -3, and -4 in mammals) and homologues of Drosophila Serrate (Jagged-1 and -2 in mammals). Jagged ligands have an additional, cysteine-rich region proximal to the trans-membrane segment. Within the same ligand type, the intracellular region of Notch ligands is well conserved through evolution, while different ligand types show quite distinct cytoplasmic tails. From multiple sequence alignments, the presence of relatively well distinct groups can be identified (Figure 2 and Figures 3, 4, 5, 6, 7). These groups include orthologues of human Jagged-1 (J1), of human Jagged-2 (J2), of human Delta-1 (D1) and Delta-4 (D4). Two additional, more heterogenous groups include orthologues of human Delta-3 (D3) and other more distantly related ligands. Groups J1 and J2 make a superfamily, as well as groups D1 and D4. Group D3 sits somewhat apart, and cannot be reliably assigned to any superfamily. Indeed, some of the sequences cannot be assigned to a definite group with high enough confidence. While the intracellular region of Drosophila Serrate does appear to be related to the J1 and J2 groups, Drosophila Delta is only distantly related to the D1 and D4 groups. In a similar way, C. elegans LAG2 can be assigned to the D3 group with low confidence and APX1 is only distantly related to the D1 and D4 groups. It can be remarked that sequence conservation is not limited to the C-terminal, PDZ-interacting motif, but extends well beyond the C-terminal residues. Predictions supported by preliminary experimental results [17] point towards a mainly disordered nature for Notch ligands cytoplasmic tail (Figure 8). On the other hand, sequence conservation within ligand types suggests that precise sequence characteristics might be required for specific patterns of post-translational modifications to take place and for specific protein-protein interactions to occur.

Figure 1
figure 1

Domain architecture of Notch ligands. Typical domain organization of Notch ligands: MNLL, N-terminal domain; DSL, Delta/Serrate Ligand domain; EGF, Epidermal Growth Factor repeat; VWC, von Willebrand Factor type C domain. The transmembrane segment is shown as a blue bar. The number and type of EGF repeats can vary.

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Figure 2
figure 2

Sequence analysis. The intracellular regions of Notch ligands from different organisms were aligned automatically using ClustalW (score matrix: Gonnet, penalty for gap opening, 10; penalty for gap closing, 1; penalty for gap extension, 0.2; penalty for gap separation, 8). The cladogram was generated using the neighbor joining algorithm and drawn using Mega [41]. Confidence values for grouping in the tree were obtained by bootstrapping (N = 1000) and normalized to 100. Identified groups are labelled as J1, J2, D1, D4, D3, and colored accordingly. The branching points between J1 and J2 and between D1 and D4 groups are also labeled. Ligands sharing the same architecture in the extracellular regions are enclosed in brackets. Similar results were obtained using T-Coffee [42] and MUSCLE [43].

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Figure 3
figure 3

Sequence alignment, group J1. Sequences were aligned using ClustalW and colored using CINEMA. Acidic residues (D, E) in red; basic (K, R) in blue; histidines (H) in light blue; aliphatic (A, V, L, I, M) in white; small hydrophobic (G, P) in orange; aromatic (F, Y, W) in magenta; hydroxyl-containing (S, T) in dark green; amide containing (N, Q) in light green; cysteines (C) in yellow.

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Figure 4
figure 4

Sequence alignment, group J2. Sequences were aligned using ClustalW and colored using CINEMA. Acidic residues (D, E) in red; basic (K, R) in blue; histidines (H) in light blue; aliphatic (A, V, L, I, M) in white; small hydrophobic (G, P) in orange; aromatic (F, Y, W) in magenta; hydroxyl-containing (S, T) in dark green; amide containing (N, Q) in light green; cysteines (C) in yellow.

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Figure 5
figure 5

Sequence alignment, group D1. Sequences were aligned using ClustalW and colored using CINEMA. Acidic residues (D, E) in red; basic (K, R) in blue; histidines (H) in light blue; aliphatic (A, V, L, I, M) in white; small hydrophobic (G, P) in orange; aromatic (F, Y, W) in magenta; hydroxyl-containing (S, T) in dark green; amide containing (N, Q) in light green; cysteines (C) in yellow.

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Figure 6
figure 6

Sequence alignment, group D4. Sequences were aligned using ClustalW and colored using CINEMA. Acidic residues (D, E) in red; basic (K, R) in blue; histidines (H) in light blue; aliphatic (A, V, L, I, M) in white; small hydrophobic (G, P) in orange; aromatic (F, Y, W) in magenta; hydroxyl-containing (S, T) in dark green; amide containing (N, Q) in light green; cysteines (C) in yellow.

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Figure 7
figure 7

Sequence alignment, group D3. Sequences (from mammals only) were aligned using ClustalW and colored using CINEMA. Acidic residues (D, E) in red; basic (K, R) in blue; histidines (H) in light blue; aliphatic (A, V, L, I, M) in white; small hydrophobic (G, P) in orange; aromatic (F, Y, W) in magenta; hydroxyl-containing (S, T) in dark green; amide containing (N, Q) in light green; cysteines (C) in yellow.

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Figure 8
figure 8

Intrinsic disorder. Disorder in the extracellular (black circles/bars) and intracellular (red circles/bars) regions of Notch ligands are shown as (a) a plot of the mean net charge v. the mean hydrophobicity [44] and (b) as the percentage of disordered residues calculated by DisEMBL using the "hot loops" definition [45]. In (a), the border between folded and natively unfolded proteins is drawn as a line.

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Predictions of phosphorylation, O-glycosylation with β-N-acetylglucosamine, and ubiquitination sites, as well as protein-protein interaction motifs, are shown for the cytoplasmic tail of human Notch ligands in Figure 9. It can be speculated that specific protein-protein interaction motifs on different ligands can specify different interaction patchworks. For example, PDZ-binding motifs are predicted for Jagged-1, Delta1, and Delta-4, but not for Jagged-2 and Delta-3; SH2-binding motifs are predicted for Jagged-1, Delta-1, and Delta-3, but not for Jagged-2 and Delta-4. Different phosphorylation patterns may also drive different protein interaction networks. The main experimental findings are summarized hereafter and shown in Figure 10.

Figure 9
figure 9

Functional analysis. Potential binding sites and post-translational modifications predicted by ELM [46, 47], NetPhos [46], and O-glycosylation [48] for the cytoplasmic tail of human Notch ligands. Prediction of ubiquitination sites is based on the preference for acidic residues adjacent to the target lysine [49]. 14-3-3, 14-3-3 proteins interacting motif (Ser/Thr phosphorylation required); Cyc, cyclin binding site; FHA, forkhead-associated domain interaction motif 1 (Thr phosphorylation required); PDZ, class I, II, or III PDZ binding motif; SH2, Src Homology 2 (SH2) domains interaction motif (tyrosine phosphorylation required; subtypes include GRB2, SH-PTP2, SRC, STAT3, STAT5, STAT6); SH3, SH3 domains binding motif (subtypes include class I, class II, and other non-canonical motifs); TRAF2, tumor necrosis factor receptor associated protein binding motif; Ub, ubiquitination site; WW, WW domain binding motif (subtypes include Group I (PPXY), Group II (PPLP), Group III, and Group IV, which requires Ser/Thr phosphorylation). Tyrosine-based sorting signals responsible for the interaction with the μ subunit of the AP (Adaptor Protein) complex are shown as doughnuts. Potential phosphorylation sites are in red; kinases are abbreviated as follows: CDK, Ser/Thr cyclin dependent kinase; CK1, casein kinase 1; CK2, casein kinase 2; GSK3, glycogen synthase kinase 3; PKA, protein kinase A; PKB, protein kinase B; PDK, Proline-Directed Kinase; PLK, Polo-like-kinase. ITIM, immunoreceptor tyrosine-based inhibitory motif (tyrosine phosphorylation required); ITSM, immunoreceptor tyrosine-based switch motif (tyrosine phosphorylation required). Sites that are candidates for O-glycosylation with β-N-acetylglucosamine are shown as grey diamonds; sites that are predicted to be both glycosylated and phosphorylated are shown as black diamonds.

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Figure 10
figure 10

Interaction network. Summary of experimentally verified interactions for the intracellular region of human or rodent Notch ligands. Proteases are shown as octagons, PDZ-containing proteins as hexagons, E3-ubiquitin ligases as diamonds, transcription factors as smoothed squares; the AP1 enhancer element is shown as a square; phosphorylation of Delta-1 by an unknown kinase (Kin) is also shown. Interactions expected by similarity as shown as dotted lines. The graph was drawn using Cytoscape [50].

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The cytoplasmic tail couples Notch ligands to PDZ-containing proteins

Independent on the interaction with receptors, the cytoplasmic tail of Notch ligands couples the Notch signal transduction machinery to PDZ containing, membrane associated proteins that play a role in the organization of cell-cell junctions. Jagged-1 has been shown to interact with the unique PDZ domain of the ras-binding protein afadin (AF6) in a PDZ-dependent manner [18, 19]. Dlg1, the human homolog of the Drosophila Discs Large protein, was identified through peptide-affinity chromatography as a binding partner for Delta-1 and -4 [20]. It was shown that Delta-1/4 can recruit Dlg1 at cell-cell junctions, tighting cell contacts and reducing cell motility [20]. The interaction is PDZ-dependent, although it was not determined which of the three PDZ domains in Dlg1 mediates this interaction. In similar studies, the interaction between Delta-1 and members of the MAGI family (M embrane A ssociated G uanylate K inases with I nverted domain arrangement) has been reported [21, 22]. The interaction specifically occurs between the C-terminus of the Delta proteins and the fourth PDZ domain of MAGIs. As there are over 300 human proteins containing at least one PDZ domain [16, 23], it is not clear yet whether specific recognition relies on subtle differences in the PDZ domains [24], on a binding region larger then the canonical, C-terminal PDZ-binding tetrapeptide [25], or both. It can be remarked that the C-terminus of Delta-3 and Jagged-2 do not contain any PDZ binding motif.

Ubiquitination of the intracellular region drives endocytosis

Extensive studies on Drosophila and other model systems [12] have shown that the cytoplasmic tail of Notch ligands undergoes ubiquitination, which in turn drives endocytosis. As endocytosis removes the ligand from the cell surface subtracting it from the interaction with the receptor, different, non-mutually exclusive models were proposed to solve this apparent contraddiction. Ligand endocytosis would create a mechanical "pulling force" on the receptor. This force would either promote a conformational change that exposes the juxtmembrane region of the receptor to proteolytic cleavage [26], thus triggering the second cleavage of the ICN, or physically dissociates the Notch heterodimer directly promoting activation [27]. It has also been proposed that ligands would be "activated" in the acidic endosomal compartments, before being recycled to the cell surface. Alternatively, ligands would cluster in multivesicular bodies before being released to the extracellular space as exosomes. Four E3 ubiquitin ligases have been identified in mammals, Mind Bomb-1 (Mib1), Mind Bomb-2 (Mib2, Skeletrophin), Neuralized-1 (Neur1) and -2 (Neur2). Mib and Neuralized proteins display different domain architectures, which might be related to their interaction with different targets: Mibs contain a HERC2/ZZ Zinc finger/HERC2 block followed by a series of ankirin repeats and two or three RING finger domains, Neur1 contains two Neuralized domains and a single RING finger, Neur2 a Neuralized domain and a Socs box. Mouse Mib1 was shown by co-immunoprecipitation to bind all Notch ligands in HEK293A cells and to promote their endocytosis in COS7 cells [28]. Knock-out [28] or mutation [29] of the Mib1 gene lead to developmental defects and death in mouse embryos. Mouse Mib2, although functionally related to Mib1, has a different expression pattern [30] and bind and ubiquitinates specifically Jagged-2, and not the other Notch ligands [31]. Knock-out of the Neur1 gene lead to viable and morphologically normal mice, yet displaying several defects [32, 33]. Finally, Neur2 was found to bind and ubiquitinate Delta-1 in HEK293A cells [34]. However, Neur2 and Mib1 displayed different subcellular localization, suggesting different and complementary roles for these two E3 ligases. Whereas in model organisms the only apparent function of the intracellular region is to carry lysine residues that can be ubiquitinylated to trigger endocytosis [35, 36], it is not clear yet whether in mammals the differences in the cytoplasmic tails are underlying more specific mechanisms to control the endocytic pathways.

Notch ligands undergo regulated intra-membrane proteolysis

It has been recently shown that in mammals Notch ligands undergo a proteolytic processing similar to that reported for Drosophila Delta and for Notch receptors. Murine Delta-1 was shown to be sequentially processed by an ADAM proteinase and by γ-secretase, the extracellular cleavage site being localized 10 residues N-terminal to the trans-membrane segment [37]. Also rat Jagged-1 [38] and human Jagged-2 [39] were shown to undergo the same type of proteolytic processing. ADAM 17 and ADAM 10 were identified as the proteinases involved in the ectodomain shedding of Jagged and Delta, respectively. The intra-membrane cleavage site has not been determined yet. In Jagged-1, it has been proposed to be placed at the first Val residue close to the cytoplasmic region [38]. The intracellular region of these ligands, after release from the cell membrane, was localized in the cytoplasm as well as in the nucleus [37–39].

The intracellular region as a membrane-tethered transcriptional regulator?

The regulated intra-membrane proteolysis, followed by the release from the membrane and the localization in the nucleus, suggests a possible role of the intracellular region in transcriptional regulation. In cotransfection studies, the intracellular region of Jagged-1 was able to promote transcription of a reporter gene in COS, CHO, and HEK cells specifically through the AP1 (Activator Protein 1, p39 jun) enhancer element [38]. Activation by Jagged-1 is at odds with AP1 repression carried out by the intracellular domain of Notch. There is no experimental evidence, however, that the intracellular region of Notch ligands can bind DNA directly and, indeed, they do not contain any recognizable DNA binding motif. More probably, they function in combination with transcriptional complexes or specific transcription factors. Evidence in this direction is given by the interaction observed between the mouse Delta-1 intracellular region and specific Smad transcription factors (Smad-2, -3, and -4) involved in TGF-β/activin signaling [40]. Interestingly, it has been noticed that one of the PDZ-containing proteins that binds Delta-1 also interacts with Activin Type 2 receptors and Smad-3 [40].

In conclusion, there is compelling evidence that bidirectional signaling is mediated by the intracellular region of Notch ligands. While the core mechanism of signal transduction mediated by Notch receptors and their ligands has been maintained through evolution, the differentiation of ligands in higher eukaryots and the unique sequence features of their intracellular region is likely to be related to specific post-translational modifications and protein-protein interaction motifs that link the Notch signaling pathway to other signaling networks. The identification of new binding partners – at the cell membrane, in the cytoplasm and in the nucleus – as well as the characterization of the post-translational modification patterns will bring new insights into this aspect of the Notch network.

Reviewers comments

Reviewer's report 1

Frank Eisenhaber, Bioinformatics Group, Institute of Molecular Pathology, Vienna, Austria

The authors present a review on the functional significance and the sequence pattern-function correlations within the intracellular part of Notch ligands. Whereas this review is of considerable interest, the authors might consider the following points for making their MS even more informative:

1) It would be good for the reader to see diagrams of the sequence architecture of representatives of the several Notch ligand classes as a figure.

2) There are many methods to evaluate and to predict intrinsically unfolded regions. The authors might wish to show to which extent segments of the notch ligand sequences do represent such reasons.

3) There are no Ying-Yang sites (except you define them, see page 4 bottom); better, speak about O-glycosylation sites.

4) The work would win from a more distinct summary with the conclusions explicitely listed.

Authors' response

1) A diagram showing the typical domain architecture of Notch ligands has been added as Figure 1.

2) Intrinsic disorder in the cytoplasmic region of Notch ligands has been calculated using two different methods. The first is based on the plot of the mean net charge v. the mean hydrophobicity, as described by Uversky et al. in ref. [44]; the second is based on DisEMBL (ref. [45]). The two methods are somewhat complementary, in that the first is based only on the amino acid composition and the physical properties of amino acid types, the second on the secondary and tertiary structure determinants in the sequence. Results have been summarized in a new figure (Figure 4a–b).

3) All potential O-glycosylation sites have now been included, independently on phosphorylation, and added in Figure 5, which has been revised accordingly.

4) Biology Direct allows only for a very short Abstract/Summary in "review" papers. Instead, we tried to list the main points in the "conclusion" paragraph.

Reviewer's report 2

L Aravind, Computational Biology Branch, NCBI, NLM, NIH, Bethesda, USA

The paper reviews the role of the Notch family ligands in signal transduction. While the role of the notch intracellular regions has been intensely investigated, the role of the intracellular portions of the corresponding ligands is less understood. In this paper Pintar et al review the current understanding of the signaling functions of the cytoplasmic tails of the DSL ligands.

The key points I have are:

1) Figure 3 shows potential modification and binding sites on the human notch ligand. Given that alignments were made for the various ligand families it will be useful to prioritize the predicted binding and PTM sites based on their conservation within a ligand family. This might indicate their greater generality in terms of a conserved signaling role.

2) "The intracellular region as a membrane-tethered transcription factor?": pg 7 of the PDF file. Is the evidence really favoring the intracellular tail as a TF itself? It is better to state that the intracellular region of the DSL ligands might function in conjunction with transcription factors. The authors might want to point out that the tail itself does not seem to have any recognizable DNA binding domains and might instead function in conjunction with a known transcription factor like SMAD.

Minor

Stylistic issue: As per BMC specifications I believe figure 2A, 2B etc need to be split up into separate figures.

"Activation by Jagged-1 is at odd with AP1 repression..."

Activation by Jagged-1 is at *odds* with AP1 repression

Page 6: The Ub E3 ligases: you might want to specify that they have RING finger domains as the active E3 component. It would also be nice if you mentioned the interesting complex domain architectures of the Mind bomb E3s in the text (or may be show it in the fig. 4)

Authors' response

1) This is an interesting observation. There are actually post-translational modifications (PTM)/bindinf motifs that are consistently predicted for all species, like the PDZ binding motifs in Jagged-1 and DLL1/DLL4, and others that are less conserved. Totally conserved motifs are likely to be strictly required for fundamental processes, whereas less conserved PTMs/binding motifs may play a role in some sort of fine tuning of the developmental processes governed by Notch signaling, and might be different in different species. From a practical point of view, it is difficult to summarize all the predictions for all species, and this is why we restricted the results to human ligands. For a reader interested in a particular PTM/binding motif, it is probably easier to jump from Figure 9 to Figures 3, 4, 5, 6, 7 to check if that feature is conserved, to what extent, and in which species.

2) We agree with the reviewer's comment. The title of the paragraph has been reformulated and we specified in the text that the intracellular region of Notch ligands may play a role in transcriptional regulation, but in an indirect manner.

Figure 2 has been splitted in separate figures.

The spelling mistake has been corrected.

E3 ubiquitin ligases: we added a short paragraph mentioning the different domain architecture of these E3 ubiquitin ligases.

Reviewer's report 3

Eugene V. Koonin, NCBI, NLM, NIH, Bethesda, USA

This is a very concise, to the point review emphasizing the diverse functions of the cytoplasmic tails of Notch ligands. The ever-growing evidence of the importance of RIP for diverse processes and the complexity of the system are remarkable.

References

  1. Ehebauer M, Hayward P, Arias AM: Notch, a universal arbiter of cell fate decisions. Science 2006, 314: 1414-1415. 10.1126/science.1134042

    Article  PubMed  CAS  Google Scholar 

  2. Weinmaster G: Notch signal transduction: a real rip and more. Curr Opin Genet Dev 2000, 10: 363-369. 10.1016/S0959-437X(00)00097-6

    Article  PubMed  CAS  Google Scholar 

  3. Rehman AO, Wang CY: Notch signaling in the regulation of tumor angiogenesis. Trends Cell Biol 2006, 16: 293-300. 10.1016/j.tcb.2006.04.003

    Article  PubMed  CAS  Google Scholar 

  4. Osborne BA, Minter LM: Notch signalling during peripheral T-cell activation and differentiation. Nat Rev Immunol 2007, 7: 64-75. 10.1038/nri1998

    Article  PubMed  CAS  Google Scholar 

  5. Chiba S: Notch signaling in stem cell systems. Stem Cells 2006, 24: 2437-2447. 10.1634/stemcells.2005-0661

    Article  PubMed  CAS  Google Scholar 

  6. Gridley T: Notch signaling and inherited disease syndromes. Hum Mol Genet 2003, 12: R9-13. 10.1093/hmg/ddg052

    Article  PubMed  CAS  Google Scholar 

  7. Roy M, Pear WS, Aster JC: The multifaceted role of Notch in cancer. Curr Opin Genet Dev 2007, 17: 52-59. 10.1016/j.gde.2006.12.001

    Article  PubMed  CAS  Google Scholar 

  8. Miele L, Golde T, Osborne B: Notch signaling in cancer. Curr Mol Med 2006, 6: 905-918. 10.2174/156652406779010830

    Article  PubMed  CAS  Google Scholar 

  9. Shih Ie M, Wang TL: Notch signaling, gamma-secretase inhibitors, and cancer therapy. Cancer Res 2007, 67: 1879-1882. 10.1158/0008-5472.CAN-06-3958

    Article  PubMed  Google Scholar 

  10. Miele L, Miao H, Nickoloff BJ: NOTCH signaling as a novel cancer therapeutic target. Curr Cancer Drug Targets 2006, 6: 313-323. 10.2174/156800906777441771

    Article  PubMed  CAS  Google Scholar 

  11. Costa RM, Drew C, Silva AJ: Notch to remember. Trends Neurosci 2005, 28: 429-435. 10.1016/j.tins.2005.05.003

    Article  PubMed  CAS  Google Scholar 

  12. Le Borgne R: Regulation of Notch signalling by endocytosis and endosomal sorting. Curr Opin Cell Biol 2006, 18: 213-222. 10.1016/j.ceb.2006.02.011

    Article  PubMed  CAS  Google Scholar 

  13. Haines N, Irvine KD: Glycosylation regulates Notch signalling. Nat Rev Mol Cell Biol 2003, 4: 786-797.

    Article  PubMed  CAS  Google Scholar 

  14. Sundaram MV: The love-hate relationship between Ras and Notch. Genes Dev 2005, 19: 1825-1839. 10.1101/gad.1330605

    Article  PubMed  CAS  Google Scholar 

  15. Kluppel M, Wrana JL: Turning it up a Notch: cross-talk between TGF beta and Notch signaling. Bioessays 2005, 27: 115-118. 10.1002/bies.20187

    Article  PubMed  Google Scholar 

  16. Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P: SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 2006, 34: D257-60. 10.1093/nar/gkj079

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  17. Popovic M, Coglievina M, Guarnaccia C, Verdone G, Esposito G, Pintar A, Pongor S: Gene synthesis, expression, purification, and characterization of human Jagged-1 intracellular region. Protein Expr Purif 2006, 47: 398-404. 10.1016/j.pep.2005.11.027

    Article  PubMed  CAS  Google Scholar 

  18. Hock B, Bohme B, Karn T, Yamamoto T, Kaibuchi K, Holtrich U, Holland S, Pawson T, Rubsamen-Waigmann H, Strebhardt K: PDZ-domain-mediated interaction of the Eph-related receptor tyrosine kinase EphB3 and the ras-binding protein AF6 depends on the kinase activity of the receptor. Proc Natl Acad Sci U S A 1998, 95: 9779-9784. 10.1073/pnas.95.17.9779

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  19. Ascano JM, Beverly LJ, Capobianco AJ: The C-terminal PDZ-ligand of JAGGED1 is essential for cellular transformation. J Biol Chem 2003, 278: 8771-8779. 10.1074/jbc.M211427200

    Article  PubMed  CAS  Google Scholar 

  20. Six EM, Ndiaye D, Sauer G, Laabi Y, Athman R, Cumano A, Brou C, Israel A, Logeat F: The notch ligand Delta1 recruits Dlg1 at cell-cell contacts and regulates cell migration. J Biol Chem 2004, 279: 55818-55826. 10.1074/jbc.M408022200

    Article  PubMed  CAS  Google Scholar 

  21. Wright GJ, Leslie JD, Ariza-McNaughton L, Lewis J: Delta proteins and MAGI proteins: an interaction of Notch ligands with intracellular scaffolding molecules and its significance for zebrafish development. Development 2004, 131: 5659-5669. 10.1242/dev.01417

    Article  PubMed  CAS  Google Scholar 

  22. Pfister S, Przemeck GK, Gerber JK, Beckers J, Adamski J, Hrabe de Angelis M: Interaction of the MAGUK family member Acvrinp1 and the cytoplasmic domain of the Notch ligand Delta1. J Mol Biol 2003, 333: 229-235. 10.1016/j.jmb.2003.08.043

    Article  PubMed  CAS  Google Scholar 

  23. Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H: PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 2005, 21: 827-828. 10.1093/bioinformatics/bti098

    Article  PubMed  CAS  Google Scholar 

  24. Basdevant N, Weinstein H, Ceruso M: Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc 2006, 128: 12766-12777. 10.1021/ja060830y

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  25. Wiedemann U, Boisguerin P, Leben R, Leitner D, Krause G, Moelling K, Volkmer-Engert R, Oschkinat H: Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J Mol Biol 2004, 343: 703-718. 10.1016/j.jmb.2004.08.064

    Article  PubMed  CAS  Google Scholar 

  26. Gordon WR, Vardar-Ulu D, Histen G, Sanchez-Irizarry C, Aster JC, Blacklow SC: Structural basis for autoinhibition of Notch. Nat Struct Mol Biol 2007, 14: 295-300. 10.1038/nsmb1227

    Article  PubMed  CAS  Google Scholar 

  27. Nichols JT, Miyamoto A, Olsen SL, D'Souza B, Yao C, Weinmaster G: DSL ligand endocytosis physically dissociates Notch1 heterodimers before activating proteolysis can occur. J Cell Biol 2007, 176: 445-458. 10.1083/jcb.200609014

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Koo BK, Lim HS, Song R, Yoon MJ, Yoon KJ, Moon JS, Kim YW, Kwon MC, Yoo KW, Kong MP, Lee J, Chitnis AB, Kim CH, Kong YY: Mind bomb 1 is essential for generating functional Notch ligands to activate Notch. Development 2005, 132: 3459-3470. 10.1242/dev.01922

    Article  PubMed  CAS  Google Scholar 

  29. Barsi JC, Rajendra R, Wu JI, Artzt K: Mind bomb1 is a ubiquitin ligase essential for mouse embryonic development and Notch signaling. Mech Dev 2005, 122: 1106-1117. 10.1016/j.mod.2005.06.005

    Article  PubMed  CAS  Google Scholar 

  30. Koo BK, Yoon KJ, Yoo KW, Lim HS, Song R, So JH, Kim CH, Kong YY: Mind bomb-2 is an E3 ligase for Notch ligand. J Biol Chem 2005, 280: 22335-22342. 10.1074/jbc.M501631200

    Article  PubMed  CAS  Google Scholar 

  31. Takeuchi T, Adachi Y, Ohtsuki Y: Skeletrophin, a novel ubiquitin ligase to the intracellular region of Jagged-2, is aberrantly expressed in multiple myeloma. Am J Pathol 2005, 166: 1817-1826.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  32. Vollrath B, Pudney J, Asa S, Leder P, Fitzgerald K: Isolation of a murine homologue of the Drosophila neuralized gene, a gene required for axonemal integrity in spermatozoa and terminal maturation of the mammary gland. Mol Cell Biol 2001, 21: 7481-7494. 10.1128/MCB.21.21.7481-7494.2001

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  33. Ruan Y, Tecott L, Jiang MM, Jan LY, Jan YN: Ethanol hypersensitivity and olfactory discrimination defect in mice lacking a homolog of Drosophila neuralized. Proc Natl Acad Sci U S A 2001, 98: 9907-9912. 10.1073/pnas.171321098

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  34. Song R, Koo BK, Yoon KJ, Yoon MJ, Yoo KW, Kim HT, Oh HJ, Kim YY, Han JK, Kim CH, Kong YY: Neuralized-2 regulates a Notch ligand in cooperation with Mind bomb-1. J Biol Chem 2006, 281: 36391-36400. 10.1074/jbc.M606601200

    Article  PubMed  CAS  Google Scholar 

  35. Itoh M, Kim CH, Palardy G, Oda T, Jiang YJ, Maust D, Yeo SY, Lorick K, Wright GJ, Ariza-McNaughton L, Weissman AM, Lewis J, Chandrasekharappa SC, Chitnis AB: Mind bomb is a ubiquitin ligase that is essential for efficient activation of Notch signaling by Delta. Dev Cell 2003, 4: 67-82. 10.1016/S1534-5807(02)00409-4

    Article  PubMed  CAS  Google Scholar 

  36. Wang W, Struhl G: Drosophila Epsin mediates a select endocytic pathway that DSL ligands must enter to activate Notch. Development 2004, 131: 5367-5380. 10.1242/dev.01413

    Article  PubMed  CAS  Google Scholar 

  37. Six E, Ndiaye D, Laabi Y, Brou C, Gupta-Rossi N, Israel A, Logeat F: The Notch ligand Delta1 is sequentially cleaved by an ADAM protease and gamma-secretase. Proc Natl Acad Sci USA 2003, 100: 7638-7643. 10.1073/pnas.1230693100

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  38. LaVoie MJ, Selkoe DJ: The Notch ligands, Jagged and Delta, are sequentially processed by alpha-secretase and presenilin/gamma-secretase and release signaling fragments. J Biol Chem 2003, 278: 34427-34437. 10.1074/jbc.M302659200

    Article  PubMed  CAS  Google Scholar 

  39. Ikeuchi T, Sisodia SS: The Notch ligands, Delta1 and Jagged2, are substrates for presenilin-dependent "gamma-secretase" cleavage. J Biol Chem 2003, 278: 7751-7754. 10.1074/jbc.C200711200

    Article  PubMed  CAS  Google Scholar 

  40. Hiratochi M, Nagase H, Kuramochi Y, Koh CS, Ohkawara T, Nakayama K: The Delta intracellular domain mediates TGF-beta/Activin signaling through binding to Smads and has an important bi-directional function in the Notch-Delta signaling pathway. Nucleic Acids Res 2007, 35: 912-922. 10.1093/nar/gkl1128

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  41. Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 2004, 5: 150-163. 10.1093/bib/5.2.150

    Article  PubMed  CAS  Google Scholar 

  42. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302: 205-217. 10.1006/jmbi.2000.4042

    Article  PubMed  CAS  Google Scholar 

  43. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32: 1792-1797. 10.1093/nar/gkh340

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  44. Uversky VN, Gillespie JR, Fink AL: Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 2000, 41: 415-427. 10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7

    Article  PubMed  CAS  Google Scholar 

  45. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB: Protein disorder prediction: implications for structural proteomics. Structure 2003, 11: 1453-1459. 10.1016/j.str.2003.10.002

    Article  PubMed  CAS  Google Scholar 

  46. Blom N, Gammeltoft S, Brunak S: Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 1999, 294: 1351-1362. 10.1006/jmbi.1999.3310

    Article  PubMed  CAS  Google Scholar 

  47. Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ: ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 2003, 31: 3625-3630. 10.1093/nar/gkg545

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  48. Gupta R, Brunak S: Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput 2002, 310-322.

    Google Scholar 

  49. Catic A, Collins C, Church GM, Ploegh HL: Preferred in vivo ubiquitination sites. Bioinformatics 2004, 20: 3302-3307. 10.1093/bioinformatics/bth407

    Article  PubMed  CAS  Google Scholar 

  50. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13: 2498-2504. 10.1101/gr.1239303

    Article  PubMed  CAS  PubMed Central  Google Scholar 

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Acknowledgements

We apologize for not citing all the contributors to this field: only work specifically focused on mammalian systems was surveyed and only the most recent reviews were cited.

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  1. International Centre for Genetic Engineering and Biotechnology (ICGEB), Protein Structure and Bioinformatics Group, Trieste, AREA Science Park, Padriciano 99, I-34012, Italy

    Alessandro Pintar, Alfredo De Biasio, Matija Popovic & Neli Ivanova

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  1. Alessandro Pintar
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  2. Alfredo De Biasio
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  3. Matija Popovic
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Correspondence to Alessandro Pintar.

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Pintar, A., De Biasio, A., Popovic, M. et al. The intracellular region of Notch ligands: does the tail make the difference?. Biol Direct 2, 19 (2007). https://doi.org/10.1186/1745-6150-2-19

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Biology Direct

ISSN: 1745-6150

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