| Literature DB >> 22116789 |
Dinesh C Soares, Becky C Carlyle, Nicholas J Bradshaw, David J Porteous.
Abstract
Disrupted in schizophrenia 1 (DISC1) is well established as a genetic risk factor across a spectrum of psychiatric disorders, a role supported by a growing body of biological studies, making the DISC1 protein interaction network an attractive therapeutic target. By contrast, there is a relative deficit of structural information to relate to the myriad biological functions of DISC1. Here, we critically appraise the available bioinformatics and biochemical analyses on DISC1 and key interacting proteins, and integrate this with the genetic and biological data. We review, analyze, and make predictions regarding the secondary structure and propensity for disordered regions within DISC1, its protein-interaction domains, subcellular localization motifs, and the structural and functional implications of common and ultrarare DISC1 variants associated with major mental illness. We discuss signaling pathways of high pharmacological potential wherein DISC1 participates, including those involving phosphodiesterase 4 (PDE4) and glycogen synthase kinase 3 (GSK3). These predictions and priority areas can inform future research in the translational and potentially guide the therapeutic processes.Entities:
Year: 2011 PMID: 22116789 PMCID: PMC3222219 DOI: 10.1021/cn200062k
Source DB: PubMed Journal: ACS Chem Neurosci ISSN: 1948-7193 Impact factor: 4.418
Figure 1Structural overview of DISC1. Figure depicting application of a complementary suite of bioinformatics structure prediction methods on the sequence of human DISC1. These results are plotted in graphical format using an equivalent scale along the x-axis for residue position with the confidence or probability scores for each assignment along the y-axis. (a) MetaPrDOS, the “metaserver” that provides an integrated consensus disorder prediction (blue with dots) derived from seven independent disorder prediction methods. The individual prediction assignment for each method (refer to key) is also shown. (b) The PsiPred secondary structure prediction for human DISC1 (α-helices, red; β-strands, green) is provided. (c, d) Two independent coiled-coil method predictions applied to DISC1 is shown; PCOILS (input, multiple sequence alignment from Chubb et al.;[3] weight, yes; matrix, MTIDK; window, 14, 21, 28) and MarCOIL (input, human DISC1 sequence; matrix, MTIDK; TransProb, high; window, not applicable). From this figure, the dearth of secondary structure in the N-terminus of DISC1 is apparent. Various segments within the N-terminus overlap with assignments of consensus disorder tendency predictions (with a stringent false positive cutoff 2%). Also evident is the overlap between PsiPred predicted helices and the coiled-coil helices and also the occurrence of other regular α-helices within the C-terminus.
Figure 2DISC1 structure schematic, sequence variants and binding sites. (a) Schematic depicting mapped secondary structure (pink, regular α-helices; green, coiled-coil helices; light-green, ambiguous helix, maybe regular or coiled-coil) and extended consensus disorder predictions (thick yellow lines) from Figure 1, drawn to scale. Position of sequence motifs and features are highlighted; these include the nuclear localization signal (NLS), serine-phenylalanine-rich (SF-rich) motif, phosphorylation sites [pT50 (putative), pS54, pS713, brown triangles][14] and translocation break point t(1;11) at amino acid position 597.[1,2] Known mouse missense mutations (blue star), human common variants (black star), and human ultrarare mutations (red star) are indicated. Ortholog sequence conservation is shown mapped below the DISC1 schematic to represent the strength of conservation for each sequence position in DISC1 (gaps excluded); these were calculated using the program AL2CO[194] using the multiple sequence alignment from Chubb et al.,[3] but excluding the fragment sequence of that lacked the N-terminal region to avoid bias in calculation. The AL2CO conservation score was averaged over a 31 amino acid sliding window (15 residues either side of a central residue) and colored accordingly (refer scale for conservation gradient). The conservation “heat map” brings out the greater variation in the N-terminus versus the C-terminus. Apparent from this depiction are the highly conserved NLS and SF-rich motifs. Interestingly, the predicted regions of disorder map to areas of least conservation. The 13 exons that encompass full-length DISC1 are shown above the schematic. (b) Known regions of DISC1 involved in self-association and protein–protein interactions determined using truncated protein constructs are shown. Green lines indicate constructs which are sufficient for protein binding and thus include a protein binding domain. Where two or more overlapping constructs are each sufficient for interaction, the overlapping region is indicated with a solid line and the remainder with dotted lines. Red boxes indicate regions which abolish or severely impair protein binding if deleted; these may represent protein binding domains or other essential structural features. Yellow lightning bolts indicate small groups of 2–4 amino acid residues, which if mutated, abolish or reduce protein binding. Data derived from Table 1; see references therein. All lines are drawn to scale with the DISC1 structure schematic in (a).
Regions of DISC1 Important for Interaction with Its Protein-Binding Partnersa
| protein | assay type | interacting DISC1 constructs | noninteracting DISC1 constructs | refs |
|---|---|---|---|---|
| APP | OE, BL | 1–854 (L isoform), 1–402, Lv, S, and Es isoforms | 403–854* | ( |
| α-tubulin | OE, BL | 181–357 | 1–181, 358–598, 598–854 | ( |
| ATF4 | OE, RP | 1–854 | 1–854Δ(607–628), 1–854Δ(Exon9) | ( |
| ATF5 | OE | 1–854, 293–854 | 1–587, 697–854* | ( |
| BBS1, 4 and 8 | OE | 1–854, 349–600 | 1–348, 601–854 | ( |
| CAMDI | OE, BL | 446–507 | 340–400*, 533–590 | ( |
| DBZ | OE, CL, BL | 348–597, 446–633 | 598–854 | ( |
| DISC1 (self-association) | OE, RP | 1–854, 1–504, 1–536, 1–597, 402–854 | 1–402, 1–854Δ(403–504) | ( |
| DISC1 (dimers) | RP | 598–785, 640–854, 640–854Δ(748–769), 668–854, 765–854 | ( | |
| DISC1 (oligomers) | RP | 598–785, 640–854, 640–854Δ(748–769), 668–854 | 765–854 | ( |
| Dixdc1 | OE, BL | 1–852, 596–852 (mouse) | 1–220, 221–355, 356–595* (mouse) | ( |
| Dysbindin | OE, RP, post-mortem brain# | 316–854, 316–854Δ(403–504) | ( | |
| eIF3 p40 | OE, CL, RP | 1–854, 1–231, 1–347 | 1–115, 116–231, 116–347, 232–347, 349–854 | ( |
| FEZ1 | OE | 1–854, 446–633 | 1–854Δ(446–533) | ( |
| Girdin& | OE, RP, PN, BL | 1–854, 1–361, 1–597, 1–633, 1–832, 347–633, 347–854, 633–854 | 1–347, 361–832, 598–832 | ( |
| Grb2 | RP, BL | 1–854 | 1–854(mut730/731) | ( |
| GSK3β | RP, BL | 1–220, 195–238, 211–225, 356–595 (mouse) | 221–355, 596–852, other peptides within: 195–238 (mouse) | ( |
| Kal-7 | OE, PA, PN, BL | 1–853, 1–401, peptides:, 41–100, 321–355, 376–410 | 1–347, 290–853, 402–853, 1–853Δ(350–394), other peptides | ( |
| Kendrin | OE | 1–854, 446–854 | 1–854Δ(446–533), 348–597, 446–533, 446–633, 598–854 | ( |
| KIF5A | OE, CL, RP, BL | 1–832, 1–361, 1–597 | 362–832, 598–832 | ( |
| LIS1 | OE, CL | 1–854, 727–854 (data not shown) | 1–597 | ( |
| MAP1A | OE | 1–854, 1–597 | 293–854 | ( |
| MIP-T3 | OE | 1–854, 1–597, 293–854 | 687–854 | ( |
| Mitofilin | OE, RP, CL, PN, BL | 200–400, 598–854, 726–854 | 358–597*, 598–726 | ( |
| N-CoR | OE | 1–854, 1–854Δ(Exon9), 1–854Δ(Exon9–11), 1–854Δ(Exon13) | 1–854Δ(Exon9–13) | ( |
| NDE1 | OE, CL, BL | 1–854 | 1–854Δ(802–835) | ( |
| NDEL1& | OE, CL, RP, BL | 1–854, 1–835, 293–854, 598–854, 727–854 | 1–357, 1–597*, 1–597Δ(403–504), 1–697*, 1–726*, 1–738*, 1–801*, 598–854Δ(807–828), 697–854 | ( |
| PCM1 | OE | 1–854, 1–854Δ(802–835), 1–348, 601–854 | 349–600 | ( |
| PDE4B1 and 2 | OE, CL, PA | peptides: 31–65, 101–135, 196–225, 266–290, 611–650 | other peptides | ( |
| PDE4B3 | OE, CL, PA | 1–854, 1–250, 1–300, 48–854, 124–854, 190–854, 220–283, 220–854, 359–854 | 1–180, 284–854 | ( |
| PDE4D3 | OE, CL, PA | Peptides: 191–230, 611–650 | other peptides | ( |
| TNIK | OE, BL | 1–854, 1–597, 1–697, 1–726, 1–748, 1–801, 1–835, 46–854, 150–854, 245–854, 291–854, 302–854, 313–854, 324–854, 335–854 | 1–854(mut 336–338, 344), 348–854*, 403–854 | ( |
| TRIO | OE, RP | 1–852, 1–408 (mouse) | 401–645, 636–852 (mouse) | ( |
DISC1 truncation mutants, recombinant proteins, and peptides which have been tested for protein–protein interaction beyond yeast two-hybrid screening are listed, with outcome and corresponding references. Refer to Abbreviations for full names and aliases of proteins listed in Table 1. Assay type abbreviations: BL = Coimmunoprecipitation in rodent brain lysate; CL = coimmunoprecipitation in cell line; OE = coimmunoprecipitation of overexpressed protein; PA = interaction on an in vitro peptide array; PN = coimmunoprecipitation in rodent primary neurons; RP = interaction of recombinant protein in vitro (pull down assay or copurification); # = in a subset only, specifically with aggregated DISC1. Asterisks (∗) denote constructs which showed some interaction, but for which this was dramatically reduced compared to other DISC1 constructs. “Peptides” denote regions of DISC1 for which a variety of short peptides, spanning the listed region were tested. “Mut” denotes that mutation of the listed amino acids was sufficient to block interaction. For DISC1-DISC1 interaction sites, “self-association” represents regions shown to bind in cell models, while “dimers” and “oligomers” represent oligomeric states of the purified constructs. Where mouse constructs were used, these are mentioned. Where specific human DISC1 alternatively spliced isoforms were tested, these are indicated long (L isoform, 1–854 amino acids), long variant (Lv isoform), short (S isoform), and extremely short (Es isoform). The potential binding protein region summary is summarized schematically in Figure 2 drawn to scale with DISC1. Ampersands (&) denote discrepancies in noted interaction domains with DISC1; these are discussed in more detail in the text.
Figure 3DISC1 transcript splice variants and protein species. The sizes of predicted DISC1 proteins from known transcripts with protein species detected by Western blotting using anti-DISC1 antibodies are compared. First column: Black lines indicate predicted sizes of proteins encoded by each of the splice variants described by Nakata et al.[57] that were found in at least 30% of either human adult (A) or fetal (F) hippocampal samples examined. Refer to original paper for details of exon structure for each variant. Gray lines indicate the predicted sizes of variants found in a lower proportion of samples. Two short variants (22.2 kDa and 2.5 kDa, each found in single samples) are not shown. Remaining columns: Endogenous DISC1 protein species detected in human (second column), primate (third column), or rodent (fourth column) by Western blotting. Dark blue lines indicate species detected in brain tissue, and pale blue lines represent species described to date in cell lines only. Sizes indicated are as described by authors of the original papers. Where no size was estimated, protein is not shown. Notably, Ishizuka et al. also saw several 100–150 kDa species in mouse brain using a range of antibodies,[61] and Leliveld et al. detected several short (50 kDa and lower) isoforms in human brain using antibodies against the DISC1 C-terminus.[15] Human Western blot data taken from refs (15, 49, 59, 64, and 114), primate data from ref (25), and rodent data from refs (8, 59, 60, 80, 140, and 195−199).
Known or Predicted Consequences of DISC1 Protein Sequence Variation on Structure and Functiona
| sequence variant in DISC1 | sequence conservation and location on structure | experimental effects where known and potential binding region overlap | notes, motifs, and potential effects on structure and function |
|---|---|---|---|
| Human common variants | |||
| R264Q (Q264 minor allele frequency 0.2599) | R in | Binding region: APP, α-tubulin, KIF5A, MAP1A, mitofilin, PCM1, TRIO | Lies close to peptide region in DISC1 266–290 mapped as PDE4B1 binding. Loss or gain of charge alters interaction propensity? |
| L607F (F607 minor allele frequency 0.0986) | Experimental: Lower levels of the DISC1-interacting protein PCM1 at the centrosome for F607 (see main text for other details of effects of L607F). | Located directly
within a leucine zipper motif, within a heptad repeat at position
“d”. Change to Phe could alter the intricate Leu-Leu
packing between adjacent helices. The presence of repeating leucine
residues at position “d” in leucine zippers is critical
for modulating coiled-coil stability, maintaining oligomeric state,
partner selection, and orientation of coiled-coil helices as shown
by numerous substitution experiments by Harbury and co-workers on
the GCN4-zipper for its leucine positions, with other hydrophobic
residues.[ | |
| Binding region: ATF4, ATF5, Dixdc1, FEZ1, N-CoR, PCM1. | |||
| S704C (C704 minor allele frequency 0.2472) | Experimental: S704C alters NDE1, NDEL1 interaction. Structurally, C704 has on average, a moderately higher fraction of oligomers than S704. C704S implicated in altered PCM1 localization (see main text for other details of effects of S704C) | S704C lies
close (context residue) to a predicted nuclear export signal (NES).[ | |
| Binding region: DISC1 (oligomerization), Dixdc1, girdin, kendrin, N-CoR, PCM1. | |||
All known DISC1 sequence variants are tabulated. The sequence conservation information was inferred on the basis of the ortholog multiple sequence alignment shown in Chubb et al.[3]hs, ; pt, ; ma, ; bt, ; cf, ; rn, ; mo, ; tr, ; dr, . Predicted location on secondary structure was based upon annotations made using methods described in Figure 1. Minor allele frequency for human common variants obtained from dbSNP[93] (1000 Genome phase 1 genotype data, release 08/04/2010). Binding region information obtained from the literature (refer to Table 1 and Figure 2).
DISC1 Subcellular Localizationa
| cellular location | details and associated functions of DISC1 | refs |
|---|---|---|
| Centrosome | Involved in recruitment of kendrin, dynein, and dynactin subunits, LIS1, NDEL1, PCM1, ninein, and CAMDI to the centrosome. Also interacts here with PDE4B, PDE4D, NDE1, and BBS4. These interactions include those important in microtubule aster formation, neurite outgrowth, and neuronal migration. | ( |
| Cilia | Found at the base of primary cilia and appears to regulate their formation and/or maintenance. Knockdown of endogenous DISC1 leads to marked reduction of primary cilia. Other DISC1 interactors seen at the cilia include the BBS family and PCM1. | ( |
| Cytoskeleton | Seen along both actin filaments and microtubules. Expression of truncated DISC1 leads to a disorganized microtubule network. | ( |
| Growth cones | Found here in the hippocampus and is involved in recruiting proteins including LIS1, NDEL1, 14-3-3ε, and girdin via kinesin-based transport along the cytoskeleton. Also important for axonal elongation. | ( |
| Membranes | Found in membrane fractions where it interacts with APP, which is important in cortical precursor formation. | ( |
| Mitochondria | Found at mitochondria present on microtubules and regulates their trafficking. Can cause mitochondria to form “ring” structures. Interacts with mitofilin within the mitochondria and is required for correct electron transport chain, monoamine oxidase, and Ca2+ activity. | ( |
| Nucleus | Found at the chromatin,
promyelocytic leukemia bodies, and outer layers of nuclear membrane.
Represses ATF4 transcriptional activity and transcription of N-cadherin
and alters sleep homeostasis in | ( |
| Synapse | Seen at the postsynaptic density along with PDE4 and NDE1. Interacts with and inhibits TNIK here, leading to degradation of key synaptic proteins. Also affects dendritic spine formation through modulation of PSD-95/Kal-7/Rac1 complexes here. | ( |
The regions where DISC1 has been shown to localize are provided, along with summary details of known roles or associated functions therein.
Figure 4DISC1 therapeutic pathways. Neurologically relevant cellular signaling pathways influenced by DISC1 are shown. Green arrows depict activation enzymes, or otherwise enhancement of the target functions (for example, by leading to upregulated transcription of the protein). Red arrows depict inhibition or otherwise downregulation. Black arrows depict effects which do not fall easily into one of the above categories or that are not yet fully understood. Data on the role of DISC1 in these pathways was taken from refs (9−11, 36, 37, 70, 71, 98, 131, 158, and 200). Dashed arrows indicate indirect effects. Refer Abbreviations for full names and text for further details.