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highly conserved C-terminal PAX6 peptide\nWe and others [31-33] noted that there is significant sequence conservation at the C-terminal end of the PAX6 protein. BLAST analysis of the amino acid sequence of the PAX6 PST domain (aa 278–422) revealed a highly conserved motif within the last 28 amino acids (beginning at the 'GLISP' motif, Figure 1a). Strong conservation was seen in distantly related species such as axolotl (Ambystoma mexicanum) and sea urchin (Paracentrotus lividus) (Figure 1a).\nFigure 1 Characterisation of the PAX6 C-terminal peptide. (a) CLUSTAL alignment of the terminal 42 amino acids of PAX6 from diverse species. (*) indicates invariant residues, (:) indicates highly similar substitutions and (.) indicates moderately similar substitutions. (b) Secondary structure analysis of the highly conserved terminal 28 amino acids predicts a single beta sheet (arrow) in the SVPVQ peptide. (c) When 4 residues are added in the N-terminal direction, 2 beta sheets are now predicted. We subjected the whole PAX6 PST domain to secondary structure analysis using JPRED, a program that uses a number of different protein structure prediction algorithms to generate a consensus secondary structure (Figure 1) [25,26]. The PST domain was largely devoid of predicted secondary structure except for the C-terminal region, which contained two predicted beta sheets within the highly conserved domain, one in the 'GLISP' motif and one in the 'SPVPQ' motif (identical to the pattern shown in Figure 1c). Initially we defined the C-terminal domain as running from the 'GLISP' motif up to the stop codon, since this region was most highly conserved and contained strongly predicted secondary structure elements. However when we performed secondary structure prediction analysis on this 28 amino acid peptide, the first beta sheet was lost (Figure 1b). Addition of another 4 amino acids (TTST) immediately before 'GLISP' caused recovery of the first beta sheet (Figure 1c). Although these 4 residues are not highly conserved (Figure 1a), they appear to be important for seeding the first beta sheet and therefore for secondary structure. Thus we define the C-terminal peptide as being the final 32 amino acids of PAX6, running from threonine 391 to the stop codon (top line of Figure 1c).\n\nYeast two-hybrid screening\nWe hypothesised that the C-terminal peptide might be involved in protein-protein interactions, and we tested this by screening a cDNA library using the yeast two-hybrid system with a construct (PAX6CTP) in which the 32 amino acid C-terminal peptide was fused to the yeast GAL4 DNA binding domain. We chose to screen a mouse brain cDNA library as no human libraries were available. Given the fact that the amino acid sequence of the PAX6 protein is identical in man and mouse, we reasoned that a mouse brain library would yield relevant interactors. For comparison we also carried out the screen using a construct containing the whole PST domain (PAX6PST).\nThe C-terminal peptide screen gave 15 colonies that were positive with all three reporters and the PST domain screen gave 62 colonies. The interacting plasmids were isolated and the cDNA inserts sequenced. Three cDNAs were identified 3 or more times, Homer3 (NM_011984), Dncl1 (Dynein cytoplasmic light chain 1, NM_019682, also known as Pin or Dlc8) and Trim11 (Tripartite motif protein family member 11, NM_053168). Homer3 (6 clones) and Dncl1 (2 clones) were identified in the C-terminal peptide screen. Homer3 (7 clones), Dncl1 (2 clones) and Trim11 (6 clones) were identified in the PST domain screen. All cDNA inserts were in-frame with the coding region of the pPC86 GAL4 activation domain. None of the cDNAs was present in a list of known false positives [34].\nHOMER3 is a member of the HOMER family of neuronal post-synaptic density (PSD) proteins [35]. DNCL1 is a subunit of two motor protein complexes, dynein and myosin-Va, both of which are involved in intracellular trafficking of proteins and organelles in neurons [36,37]. TRIM11 is a member of the tripartite motif protein family and contains a RING finger, a B-box zinc finger, a coiled coil domain and a B30.2 domain [38]. The possible significance of the interactions between these proteins and PAX6 is discussed below.\n\nSemi-quantitative PCR\nTo check that the Homer3, Dncl1 and Trim11 clones were not identified multiple times solely because they are highly abundant in the library, we performed a semi-quantitative PCR assay. We compared the relative abundance of Homer3, Dncl1, Trim11 and Pax6 with Gapdh and Atp5a1. Gapdh and Atp5a1 both show strong constitutive expression in a variety of tissues including the brain [29,30]. Homer3, Dncl1, Trim11 and Pax6 were only amplified strongly after 35 cycles of PCR (Figure 2) and were therefore present at relatively low levels compared to Gapdh (amplified strongly after 25 cycles) and Atp5a1 (amplified strongly after 30 cycles; Figure 2).\nFigure 2 Semi-quantitative PCR analysis of Homer3, Dncl1, Trim11 and Pax6 in the mouse brain cDNA library. Library cDNA was amplified with primers specific for Pax6 (600 bp), Homer3 (485 bp band), Dncl1 (485 bp) and Trim11 (609 bp) for 20, 25, 30 or 35 cycles. Atp5a1 (415 bp) and Gapdh (450 bp), which are highly expressed in the brain, are included for comparison. M indicates the Φ×174 HaeIII DNA size marker; the positions of the 603 bp and 310 bp marker bands are indicated. We concluded that Homer3, Dncl1 and Trim11 clones were not highly abundant in the library. This is consistent with the idea that they were pulled out because the encoded proteins interact specifically with the C-terminal peptide or PST domain of PAX6.\n\nYeast two-hybrid pairwise interactions\nBy library screening we identified two proteins (HOMER3 and DNCL1) that interact with the C-terminal peptide and three proteins (HOMER3, DNCL1 and TRIM11) that interact with the whole PST domain. This suggests that HOMER3 and DNCL1 interact specifically with the C-terminal peptide while TRIM11 interacts with a more N-terminal part of the PST domain. We conducted pairwise tests between specific constructs to confirm the interactions identified in the library screen and to further investigate the interaction between PAX6 and HOMER3, DNCL1 and TRIM11. The Dncl1 and Trim11 clones that were pulled out of the library were full-length, but the Homer3 cDNAs lacked the N-terminal 70 amino acids. The missing coding region was inserted into the truncated Homer3 cDNA to give a full-length expression construct (see Methods). Pairwise interactions were carried out with both the full-length and truncated Homer3 clones.\nWe confirmed that the whole PAX6 PST domain interacts with HOMER3 (full-length and truncated constructs), TRIM11 and DNCL1, as all three reporter genes were strongly activated in pairwise tests (Figure 3; Table 1). In contrast the interaction between the C-terminal peptide and HOMER3 or DNCL1 could not be confirmed with pairwise tests (Table 1). Occasionally, partial suppression of growth on plates containing 5-fluoro-orotic acid was observed, indicating low-level activation of the URA3 reporter; however HIS3 and LacZ activation were not observed. The reasons for this are not clear, although it may be that the pairwise tests were of sub-optimal sensitivity compared to the library screen. However we were able to confirm that the C-terminal peptide is important for the interaction with HOMER3 and DNCL1 because interaction with the PAX6PST-CT construct, which lacks the final 32 amino acids, was completely abolished (Figure 3, Table 1). TRIM11 interacted equally well with PAX6PST and PAX6PST-CT (Figure 3, Table 1). This is consistent with the library screens in which TRIM11 was isolated with the PST domain but not with the C-terminal peptide and supports the idea that the C-terminal peptide is not important for the interaction between PAX6 and TRIM11.\nFigure 3 LacZ reporter gene activation in pairwise tests. pPC86 constructs are shown across the top, and pDBLeu constructs are shown down the right hand side. PAX6PST, PAX6 PST domain; PAX6PST/Q422R, PAX6 PST domain with the Q422R mutation; PAX6PST/X423L, PAX6 PST domain with the X423L mutation, PAX6PST/1615del10, PAX6 PST domain with the 1615 del10 mutation; PAX6PST-CT, PAX6 PST domain minus the C-terminal peptide. 'Truncated HOMER3' is HOMER3 lacking the N-terminal 70 amino acids. Five control strains are shown for comparison (left). These range from non-interactor (A) to strong interactor (E).\nTable 1 Pairwise interaction tests between normal and mutant PAX6 constructs and HOMER3, DNCL1 and TRIM11. +++: strong interaction; ++: moderate interaction; +: weak interaction; (+) borderline interaction with one or two reporters activated at very low levels; 0: no interaction. PAX6PST, PAX6 PST domain; PAX6CTP, PAX6 C-terminal peptide; PAX6PST-CT, PAX6 PST domain minus the C-terminal peptide; PAX6PST/Q422R, PAX6 PST domain with the Q422R mutation; PAX6PST/X423L, PAX6 PST domain with the X423L mutation, PAX6PST/1615del, PAX6 PST domain with the 1615 del10 mutation. HOMER3-FL, HOMER3 full-length clone; HOMER3-Tr, truncated HOMER3 clone lacking the N-terminal 70 amino acids.\npDBLeu constructs pPC86 constructs\nHOMER3-FL HOMER3-Tr DNCL1 TRIM11\nPAX6PST +++ ++ ++ ++\nPAX6CTP 0 0 0 0\nPAX6PST-CT (+) 0 0 ++\nPAX6PST/Q422R ++ + + ++\nPAX6PST/X423L + 0 (+) ++\nPAX6PST/1615del10 (+) 0 0 ++ Having confirmed that HOMER3, DNCL1 and TRIM11 interact with the PAX6 PST domain, we next investigated how the interactions were affected by three C-terminal PAX6 mutations that have been previously described in patients with ocular anomalies. The first mutation is a single nucleotide substitution 1627A\u003eG that causes a glutamine to arginine amino acid substitution in the last codon of PAX6. This missense mutation (Q422R) has been reported in two patients, one affected by anterior segment dysgenesis with uveal ectropion and one with typical aniridia and foveal hypoplasia [27,33].\nThe second mutation (1615del10) was found in an aniridia family [28]. This frame-shifting deletion occurs just before the PAX6 stop codon and is predicted to cause translational read-through into the 3' untranslated region, generating a protein in which the last 5 amino acids of the C-terminal peptide are replaced by a 103 amino acid-extension. Affected individuals in this family showed unusual neurobehavioural traits including impaired social cognition and poor verbal inhibition [28]. MRI analysis revealed grey matter abnormalities in the frontal lobe, temporal lobe and cerebellum, and white matter deficits in the corpus callosum [13].\nThe third mutation 1629insT (X423L) has been reported in several aniridia patients [11,12,27,33]. Insertion of a single T nucleotide at position 1629 changes the stop codon (TAA) to a leucine codon (TTA) and generates a full length PAX6 protein with a C-terminal extension that extends for a further 35 amino acids into the 3' untranslated region. MRI analysis of six patients with this mutation revealed variable brain defects including absence or hypoplasia of the anterior commissure, pineal gland and olfactory bulbs [12]. Two patients had temporal polymicrogyria, one in association with epilepsy [12].\nThe three mutations were introduced into the PAX6PST construct, and pairwise tests were carried out to investigate the interaction of each mutant protein with HOMER3, DNCL1 and TRIM11. All three mutations had a clear effect on the interactions. The most subtle mutation (Q422R) caused a reduction in the interaction with HOMER3 and DNCL1 (Figure 3, Table 1). The C-terminal extension mutations X423L and1615del10 mutations both dramatically reduced or abolished the interaction with HOMER3 and DNCL1 (Figure 3, Table 1).\nNone of the three mutations affected the interaction with TRIM11 which again is consistent with the hypothesis that TRIM11 interacts with a more N-terminal part of the PST domain."}

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highly conserved C-terminal PAX6 peptide\nWe and others [31-33] noted that there is significant sequence conservation at the C-terminal end of the PAX6 protein. BLAST analysis of the amino acid sequence of the PAX6 PST domain (aa 278–422) revealed a highly conserved motif within the last 28 amino acids (beginning at the 'GLISP' motif, Figure 1a). Strong conservation was seen in distantly related species such as axolotl (Ambystoma mexicanum) and sea urchin (Paracentrotus lividus) (Figure 1a).\nFigure 1 Characterisation of the PAX6 C-terminal peptide. (a) CLUSTAL alignment of the terminal 42 amino acids of PAX6 from diverse species. (*) indicates invariant residues, (:) indicates highly similar substitutions and (.) indicates moderately similar substitutions. (b) Secondary structure analysis of the highly conserved terminal 28 amino acids predicts a single beta sheet (arrow) in the SVPVQ peptide. (c) When 4 residues are added in the N-terminal direction, 2 beta sheets are now predicted. We subjected the whole PAX6 PST domain to secondary structure analysis using JPRED, a program that uses a number of different protein structure prediction algorithms to generate a consensus secondary structure (Figure 1) [25,26]. The PST domain was largely devoid of predicted secondary structure except for the C-terminal region, which contained two predicted beta sheets within the highly conserved domain, one in the 'GLISP' motif and one in the 'SPVPQ' motif (identical to the pattern shown in Figure 1c). Initially we defined the C-terminal domain as running from the 'GLISP' motif up to the stop codon, since this region was most highly conserved and contained strongly predicted secondary structure elements. However when we performed secondary structure prediction analysis on this 28 amino acid peptide, the first beta sheet was lost (Figure 1b). Addition of another 4 amino acids (TTST) immediately before 'GLISP' caused recovery of the first beta sheet (Figure 1c). Although these 4 residues are not highly conserved (Figure 1a), they appear to be important for seeding the first beta sheet and therefore for secondary structure. Thus we define the C-terminal peptide as being the final 32 amino acids of PAX6, running from threonine 391 to the stop codon (top line of Figure 1c).\n\nYeast two-hybrid screening\nWe hypothesised that the C-terminal peptide might be involved in protein-protein interactions, and we tested this by screening a cDNA library using the yeast two-hybrid system with a construct (PAX6CTP) in which the 32 amino acid C-terminal peptide was fused to the yeast GAL4 DNA binding domain. We chose to screen a mouse brain cDNA library as no human libraries were available. Given the fact that the amino acid sequence of the PAX6 protein is identical in man and mouse, we reasoned that a mouse brain library would yield relevant interactors. For comparison we also carried out the screen using a construct containing the whole PST domain (PAX6PST).\nThe C-terminal peptide screen gave 15 colonies that were positive with all three reporters and the PST domain screen gave 62 colonies. The interacting plasmids were isolated and the cDNA inserts sequenced. Three cDNAs were identified 3 or more times, Homer3 (NM_011984), Dncl1 (Dynein cytoplasmic light chain 1, NM_019682, also known as Pin or Dlc8) and Trim11 (Tripartite motif protein family member 11, NM_053168). Homer3 (6 clones) and Dncl1 (2 clones) were identified in the C-terminal peptide screen. Homer3 (7 clones), Dncl1 (2 clones) and Trim11 (6 clones) were identified in the PST domain screen. All cDNA inserts were in-frame with the coding region of the pPC86 GAL4 activation domain. None of the cDNAs was present in a list of known false positives [34].\nHOMER3 is a member of the HOMER family of neuronal post-synaptic density (PSD) proteins [35]. DNCL1 is a subunit of two motor protein complexes, dynein and myosin-Va, both of which are involved in intracellular trafficking of proteins and organelles in neurons [36,37]. TRIM11 is a member of the tripartite motif protein family and contains a RING finger, a B-box zinc finger, a coiled coil domain and a B30.2 domain [38]. The possible significance of the interactions between these proteins and PAX6 is discussed below.\n\nSemi-quantitative PCR\nTo check that the Homer3, Dncl1 and Trim11 clones were not identified multiple times solely because they are highly abundant in the library, we performed a semi-quantitative PCR assay. We compared the relative abundance of Homer3, Dncl1, Trim11 and Pax6 with Gapdh and Atp5a1. Gapdh and Atp5a1 both show strong constitutive expression in a variety of tissues including the brain [29,30]. Homer3, Dncl1, Trim11 and Pax6 were only amplified strongly after 35 cycles of PCR (Figure 2) and were therefore present at relatively low levels compared to Gapdh (amplified strongly after 25 cycles) and Atp5a1 (amplified strongly after 30 cycles; Figure 2).\nFigure 2 Semi-quantitative PCR analysis of Homer3, Dncl1, Trim11 and Pax6 in the mouse brain cDNA library. Library cDNA was amplified with primers specific for Pax6 (600 bp), Homer3 (485 bp band), Dncl1 (485 bp) and Trim11 (609 bp) for 20, 25, 30 or 35 cycles. Atp5a1 (415 bp) and Gapdh (450 bp), which are highly expressed in the brain, are included for comparison. M indicates the Φ×174 HaeIII DNA size marker; the positions of the 603 bp and 310 bp marker bands are indicated. We concluded that Homer3, Dncl1 and Trim11 clones were not highly abundant in the library. This is consistent with the idea that they were pulled out because the encoded proteins interact specifically with the C-terminal peptide or PST domain of PAX6.\n\nYeast two-hybrid pairwise interactions\nBy library screening we identified two proteins (HOMER3 and DNCL1) that interact with the C-terminal peptide and three proteins (HOMER3, DNCL1 and TRIM11) that interact with the whole PST domain. This suggests that HOMER3 and DNCL1 interact specifically with the C-terminal peptide while TRIM11 interacts with a more N-terminal part of the PST domain. We conducted pairwise tests between specific constructs to confirm the interactions identified in the library screen and to further investigate the interaction between PAX6 and HOMER3, DNCL1 and TRIM11. The Dncl1 and Trim11 clones that were pulled out of the library were full-length, but the Homer3 cDNAs lacked the N-terminal 70 amino acids. The missing coding region was inserted into the truncated Homer3 cDNA to give a full-length expression construct (see Methods). Pairwise interactions were carried out with both the full-length and truncated Homer3 clones.\nWe confirmed that the whole PAX6 PST domain interacts with HOMER3 (full-length and truncated constructs), TRIM11 and DNCL1, as all three reporter genes were strongly activated in pairwise tests (Figure 3; Table 1). In contrast the interaction between the C-terminal peptide and HOMER3 or DNCL1 could not be confirmed with pairwise tests (Table 1). Occasionally, partial suppression of growth on plates containing 5-fluoro-orotic acid was observed, indicating low-level activation of the URA3 reporter; however HIS3 and LacZ activation were not observed. The reasons for this are not clear, although it may be that the pairwise tests were of sub-optimal sensitivity compared to the library screen. However we were able to confirm that the C-terminal peptide is important for the interaction with HOMER3 and DNCL1 because interaction with the PAX6PST-CT construct, which lacks the final 32 amino acids, was completely abolished (Figure 3, Table 1). TRIM11 interacted equally well with PAX6PST and PAX6PST-CT (Figure 3, Table 1). This is consistent with the library screens in which TRIM11 was isolated with the PST domain but not with the C-terminal peptide and supports the idea that the C-terminal peptide is not important for the interaction between PAX6 and TRIM11.\nFigure 3 LacZ reporter gene activation in pairwise tests. pPC86 constructs are shown across the top, and pDBLeu constructs are shown down the right hand side. PAX6PST, PAX6 PST domain; PAX6PST/Q422R, PAX6 PST domain with the Q422R mutation; PAX6PST/X423L, PAX6 PST domain with the X423L mutation, PAX6PST/1615del10, PAX6 PST domain with the 1615 del10 mutation; PAX6PST-CT, PAX6 PST domain minus the C-terminal peptide. 'Truncated HOMER3' is HOMER3 lacking the N-terminal 70 amino acids. Five control strains are shown for comparison (left). These range from non-interactor (A) to strong interactor (E).\nTable 1 Pairwise interaction tests between normal and mutant PAX6 constructs and HOMER3, DNCL1 and TRIM11. +++: strong interaction; ++: moderate interaction; +: weak interaction; (+) borderline interaction with one or two reporters activated at very low levels; 0: no interaction. PAX6PST, PAX6 PST domain; PAX6CTP, PAX6 C-terminal peptide; PAX6PST-CT, PAX6 PST domain minus the C-terminal peptide; PAX6PST/Q422R, PAX6 PST domain with the Q422R mutation; PAX6PST/X423L, PAX6 PST domain with the X423L mutation, PAX6PST/1615del, PAX6 PST domain with the 1615 del10 mutation. HOMER3-FL, HOMER3 full-length clone; HOMER3-Tr, truncated HOMER3 clone lacking the N-terminal 70 amino acids.\npDBLeu constructs pPC86 constructs\nHOMER3-FL HOMER3-Tr DNCL1 TRIM11\nPAX6PST +++ ++ ++ ++\nPAX6CTP 0 0 0 0\nPAX6PST-CT (+) 0 0 ++\nPAX6PST/Q422R ++ + + ++\nPAX6PST/X423L + 0 (+) ++\nPAX6PST/1615del10 (+) 0 0 ++ Having confirmed that HOMER3, DNCL1 and TRIM11 interact with the PAX6 PST domain, we next investigated how the interactions were affected by three C-terminal PAX6 mutations that have been previously described in patients with ocular anomalies. The first mutation is a single nucleotide substitution 1627A\u003eG that causes a glutamine to arginine amino acid substitution in the last codon of PAX6. This missense mutation (Q422R) has been reported in two patients, one affected by anterior segment dysgenesis with uveal ectropion and one with typical aniridia and foveal hypoplasia [27,33].\nThe second mutation (1615del10) was found in an aniridia family [28]. This frame-shifting deletion occurs just before the PAX6 stop codon and is predicted to cause translational read-through into the 3' untranslated region, generating a protein in which the last 5 amino acids of the C-terminal peptide are replaced by a 103 amino acid-extension. Affected individuals in this family showed unusual neurobehavioural traits including impaired social cognition and poor verbal inhibition [28]. MRI analysis revealed grey matter abnormalities in the frontal lobe, temporal lobe and cerebellum, and white matter deficits in the corpus callosum [13].\nThe third mutation 1629insT (X423L) has been reported in several aniridia patients [11,12,27,33]. Insertion of a single T nucleotide at position 1629 changes the stop codon (TAA) to a leucine codon (TTA) and generates a full length PAX6 protein with a C-terminal extension that extends for a further 35 amino acids into the 3' untranslated region. MRI analysis of six patients with this mutation revealed variable brain defects including absence or hypoplasia of the anterior commissure, pineal gland and olfactory bulbs [12]. Two patients had temporal polymicrogyria, one in association with epilepsy [12].\nThe three mutations were introduced into the PAX6PST construct, and pairwise tests were carried out to investigate the interaction of each mutant protein with HOMER3, DNCL1 and TRIM11. All three mutations had a clear effect on the interactions. The most subtle mutation (Q422R) caused a reduction in the interaction with HOMER3 and DNCL1 (Figure 3, Table 1). The C-terminal extension mutations X423L and1615del10 mutations both dramatically reduced or abolished the interaction with HOMER3 and DNCL1 (Figure 3, Table 1).\nNone of the three mutations affected the interaction with TRIM11 which again is consistent with the hypothesis that TRIM11 interacts with a more N-terminal part of the PST domain."}

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highly conserved C-terminal PAX6 peptide\nWe and others [31-33] noted that there is significant sequence conservation at the C-terminal end of the PAX6 protein. BLAST analysis of the amino acid sequence of the PAX6 PST domain (aa 278–422) revealed a highly conserved motif within the last 28 amino acids (beginning at the 'GLISP' motif, Figure 1a). Strong conservation was seen in distantly related species such as axolotl (Ambystoma mexicanum) and sea urchin (Paracentrotus lividus) (Figure 1a).\nFigure 1 Characterisation of the PAX6 C-terminal peptide. (a) CLUSTAL alignment of the terminal 42 amino acids of PAX6 from diverse species. (*) indicates invariant residues, (:) indicates highly similar substitutions and (.) indicates moderately similar substitutions. (b) Secondary structure analysis of the highly conserved terminal 28 amino acids predicts a single beta sheet (arrow) in the SVPVQ peptide. (c) When 4 residues are added in the N-terminal direction, 2 beta sheets are now predicted. We subjected the whole PAX6 PST domain to secondary structure analysis using JPRED, a program that uses a number of different protein structure prediction algorithms to generate a consensus secondary structure (Figure 1) [25,26]. The PST domain was largely devoid of predicted secondary structure except for the C-terminal region, which contained two predicted beta sheets within the highly conserved domain, one in the 'GLISP' motif and one in the 'SPVPQ' motif (identical to the pattern shown in Figure 1c). Initially we defined the C-terminal domain as running from the 'GLISP' motif up to the stop codon, since this region was most highly conserved and contained strongly predicted secondary structure elements. However when we performed secondary structure prediction analysis on this 28 amino acid peptide, the first beta sheet was lost (Figure 1b). Addition of another 4 amino acids (TTST) immediately before 'GLISP' caused recovery of the first beta sheet (Figure 1c). Although these 4 residues are not highly conserved (Figure 1a), they appear to be important for seeding the first beta sheet and therefore for secondary structure. Thus we define the C-terminal peptide as being the final 32 amino acids of PAX6, running from threonine 391 to the stop codon (top line of Figure 1c).\n\nYeast two-hybrid screening\nWe hypothesised that the C-terminal peptide might be involved in protein-protein interactions, and we tested this by screening a cDNA library using the yeast two-hybrid system with a construct (PAX6CTP) in which the 32 amino acid C-terminal peptide was fused to the yeast GAL4 DNA binding domain. We chose to screen a mouse brain cDNA library as no human libraries were available. Given the fact that the amino acid sequence of the PAX6 protein is identical in man and mouse, we reasoned that a mouse brain library would yield relevant interactors. For comparison we also carried out the screen using a construct containing the whole PST domain (PAX6PST).\nThe C-terminal peptide screen gave 15 colonies that were positive with all three reporters and the PST domain screen gave 62 colonies. The interacting plasmids were isolated and the cDNA inserts sequenced. Three cDNAs were identified 3 or more times, Homer3 (NM_011984), Dncl1 (Dynein cytoplasmic light chain 1, NM_019682, also known as Pin or Dlc8) and Trim11 (Tripartite motif protein family member 11, NM_053168). Homer3 (6 clones) and Dncl1 (2 clones) were identified in the C-terminal peptide screen. Homer3 (7 clones), Dncl1 (2 clones) and Trim11 (6 clones) were identified in the PST domain screen. All cDNA inserts were in-frame with the coding region of the pPC86 GAL4 activation domain. None of the cDNAs was present in a list of known false positives [34].\nHOMER3 is a member of the HOMER family of neuronal post-synaptic density (PSD) proteins [35]. DNCL1 is a subunit of two motor protein complexes, dynein and myosin-Va, both of which are involved in intracellular trafficking of proteins and organelles in neurons [36,37]. TRIM11 is a member of the tripartite motif protein family and contains a RING finger, a B-box zinc finger, a coiled coil domain and a B30.2 domain [38]. The possible significance of the interactions between these proteins and PAX6 is discussed below.\n\nSemi-quantitative PCR\nTo check that the Homer3, Dncl1 and Trim11 clones were not identified multiple times solely because they are highly abundant in the library, we performed a semi-quantitative PCR assay. We compared the relative abundance of Homer3, Dncl1, Trim11 and Pax6 with Gapdh and Atp5a1. Gapdh and Atp5a1 both show strong constitutive expression in a variety of tissues including the brain [29,30]. Homer3, Dncl1, Trim11 and Pax6 were only amplified strongly after 35 cycles of PCR (Figure 2) and were therefore present at relatively low levels compared to Gapdh (amplified strongly after 25 cycles) and Atp5a1 (amplified strongly after 30 cycles; Figure 2).\nFigure 2 Semi-quantitative PCR analysis of Homer3, Dncl1, Trim11 and Pax6 in the mouse brain cDNA library. Library cDNA was amplified with primers specific for Pax6 (600 bp), Homer3 (485 bp band), Dncl1 (485 bp) and Trim11 (609 bp) for 20, 25, 30 or 35 cycles. Atp5a1 (415 bp) and Gapdh (450 bp), which are highly expressed in the brain, are included for comparison. M indicates the Φ×174 HaeIII DNA size marker; the positions of the 603 bp and 310 bp marker bands are indicated. We concluded that Homer3, Dncl1 and Trim11 clones were not highly abundant in the library. This is consistent with the idea that they were pulled out because the encoded proteins interact specifically with the C-terminal peptide or PST domain of PAX6.\n\nYeast two-hybrid pairwise interactions\nBy library screening we identified two proteins (HOMER3 and DNCL1) that interact with the C-terminal peptide and three proteins (HOMER3, DNCL1 and TRIM11) that interact with the whole PST domain. This suggests that HOMER3 and DNCL1 interact specifically with the C-terminal peptide while TRIM11 interacts with a more N-terminal part of the PST domain. We conducted pairwise tests between specific constructs to confirm the interactions identified in the library screen and to further investigate the interaction between PAX6 and HOMER3, DNCL1 and TRIM11. The Dncl1 and Trim11 clones that were pulled out of the library were full-length, but the Homer3 cDNAs lacked the N-terminal 70 amino acids. The missing coding region was inserted into the truncated Homer3 cDNA to give a full-length expression construct (see Methods). Pairwise interactions were carried out with both the full-length and truncated Homer3 clones.\nWe confirmed that the whole PAX6 PST domain interacts with HOMER3 (full-length and truncated constructs), TRIM11 and DNCL1, as all three reporter genes were strongly activated in pairwise tests (Figure 3; Table 1). In contrast the interaction between the C-terminal peptide and HOMER3 or DNCL1 could not be confirmed with pairwise tests (Table 1). Occasionally, partial suppression of growth on plates containing 5-fluoro-orotic acid was observed, indicating low-level activation of the URA3 reporter; however HIS3 and LacZ activation were not observed. The reasons for this are not clear, although it may be that the pairwise tests were of sub-optimal sensitivity compared to the library screen. However we were able to confirm that the C-terminal peptide is important for the interaction with HOMER3 and DNCL1 because interaction with the PAX6PST-CT construct, which lacks the final 32 amino acids, was completely abolished (Figure 3, Table 1). TRIM11 interacted equally well with PAX6PST and PAX6PST-CT (Figure 3, Table 1). This is consistent with the library screens in which TRIM11 was isolated with the PST domain but not with the C-terminal peptide and supports the idea that the C-terminal peptide is not important for the interaction between PAX6 and TRIM11.\nFigure 3 LacZ reporter gene activation in pairwise tests. pPC86 constructs are shown across the top, and pDBLeu constructs are shown down the right hand side. PAX6PST, PAX6 PST domain; PAX6PST/Q422R, PAX6 PST domain with the Q422R mutation; PAX6PST/X423L, PAX6 PST domain with the X423L mutation, PAX6PST/1615del10, PAX6 PST domain with the 1615 del10 mutation; PAX6PST-CT, PAX6 PST domain minus the C-terminal peptide. 'Truncated HOMER3' is HOMER3 lacking the N-terminal 70 amino acids. Five control strains are shown for comparison (left). These range from non-interactor (A) to strong interactor (E).\nTable 1 Pairwise interaction tests between normal and mutant PAX6 constructs and HOMER3, DNCL1 and TRIM11. +++: strong interaction; ++: moderate interaction; +: weak interaction; (+) borderline interaction with one or two reporters activated at very low levels; 0: no interaction. PAX6PST, PAX6 PST domain; PAX6CTP, PAX6 C-terminal peptide; PAX6PST-CT, PAX6 PST domain minus the C-terminal peptide; PAX6PST/Q422R, PAX6 PST domain with the Q422R mutation; PAX6PST/X423L, PAX6 PST domain with the X423L mutation, PAX6PST/1615del, PAX6 PST domain with the 1615 del10 mutation. HOMER3-FL, HOMER3 full-length clone; HOMER3-Tr, truncated HOMER3 clone lacking the N-terminal 70 amino acids.\npDBLeu constructs pPC86 constructs\nHOMER3-FL HOMER3-Tr DNCL1 TRIM11\nPAX6PST +++ ++ ++ ++\nPAX6CTP 0 0 0 0\nPAX6PST-CT (+) 0 0 ++\nPAX6PST/Q422R ++ + + ++\nPAX6PST/X423L + 0 (+) ++\nPAX6PST/1615del10 (+) 0 0 ++ Having confirmed that HOMER3, DNCL1 and TRIM11 interact with the PAX6 PST domain, we next investigated how the interactions were affected by three C-terminal PAX6 mutations that have been previously described in patients with ocular anomalies. The first mutation is a single nucleotide substitution 1627A\u003eG that causes a glutamine to arginine amino acid substitution in the last codon of PAX6. This missense mutation (Q422R) has been reported in two patients, one affected by anterior segment dysgenesis with uveal ectropion and one with typical aniridia and foveal hypoplasia [27,33].\nThe second mutation (1615del10) was found in an aniridia family [28]. This frame-shifting deletion occurs just before the PAX6 stop codon and is predicted to cause translational read-through into the 3' untranslated region, generating a protein in which the last 5 amino acids of the C-terminal peptide are replaced by a 103 amino acid-extension. Affected individuals in this family showed unusual neurobehavioural traits including impaired social cognition and poor verbal inhibition [28]. MRI analysis revealed grey matter abnormalities in the frontal lobe, temporal lobe and cerebellum, and white matter deficits in the corpus callosum [13].\nThe third mutation 1629insT (X423L) has been reported in several aniridia patients [11,12,27,33]. Insertion of a single T nucleotide at position 1629 changes the stop codon (TAA) to a leucine codon (TTA) and generates a full length PAX6 protein with a C-terminal extension that extends for a further 35 amino acids into the 3' untranslated region. MRI analysis of six patients with this mutation revealed variable brain defects including absence or hypoplasia of the anterior commissure, pineal gland and olfactory bulbs [12]. Two patients had temporal polymicrogyria, one in association with epilepsy [12].\nThe three mutations were introduced into the PAX6PST construct, and pairwise tests were carried out to investigate the interaction of each mutant protein with HOMER3, DNCL1 and TRIM11. All three mutations had a clear effect on the interactions. The most subtle mutation (Q422R) caused a reduction in the interaction with HOMER3 and DNCL1 (Figure 3, Table 1). The C-terminal extension mutations X423L and1615del10 mutations both dramatically reduced or abolished the interaction with HOMER3 and DNCL1 (Figure 3, Table 1).\nNone of the three mutations affected the interaction with TRIM11 which again is consistent with the hypothesis that TRIM11 interacts with a more N-terminal part of the PST domain."}