The molecular basis of Boston-type craniosynostosis: the Pro148 -> His mutation in the N-terminal arm of the MSX2 homeodomain stabilizes DNA binding without altering nucleotide sequence preferences
The molecular basis of Boston-type craniosynostosis: the Pro148 -> His mutation in the N-terminal arm of the MSX2 homeodomain stabilizes DNA binding without altering nucleotide sequence preferencesLiang Ma+, Serge Golden, Linda Wu and Rob Maxson*
Department of Biochemistry and Molecular Biology, Kenneth R. Norris Cancer Hospital and Institute, University of Southern California School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90033, USA
Received June 24, 1996;Revised and Accepted September 23, 1996
Craniosynostosis, Boston type is an autosomal dominant disorder that results in the premature fusion of calvarial bones and ensuing abnormalities in skull shape. We showed previously that this disorder is tightly linked to the Msx2 homeobox gene on the long arm of chromosome 5, and that affected individuals bear a mutated copy of Msx2. In addition, transgenic mice in which either mutant or wild-type mouse Msx2 is overexpressed in the developing skull also exhibit craniosynostosis. That both mutant and wild-type Msx2 elicit craniosynostosis in transgenic mice and that the Boston type mutation is dominant led us to hypothesize that the mutation might enhance the normal function of Msx2. The mutation is located in position 7 of the N-terminal arm of the homeodomain, a region implicated in both target sequence recognition and protein-protein interactions. Here we test the hypothesis that the Pro148 -> His mutation alters the DNA binding properties of Msx2. Using gel shift and binding site selection analyses, we show that the mutation enhances the affinity of Msx2 for a set of known Msx2 target sequences but has little or no effect on the site specificity of Msx2 binding. The enhancement of Msx2 binding is due largely if not entirely to an increased stability of the mutant Msx2-DNA complex. These data provide a molecular-level explanation of how the Pro148 -> His mutation enhances Msx2 function and thus leads to the dominant craniosynostosis phenotype.
Craniosynostosis, the premature fusion of calvarial bones with consequent abnormalities in skull shape, is a relatively common birth defect (1/3000 live births). It has both environmental and genetic causes and is a feature in over 100 genetic syndromes (1 ,2 ). Among these is craniosynostosis, Boston-type, a highly penetrant, autosomal dominant disorder (3 ,4 ). We showed previously that individuals affected with craniosynostosis, Boston-type bear a mutated copy of Msx2, a highly conserved homeobox gene that functions in the regulation of inductive tissue interactions during embryogenesis (5 ). The mutation is a C to A transversion resulting in the substitution of a histidine for a proline in position 7 of the homeodomain (P148H). We demonstrated further that transgenic mice expressing the mutant Msx2 gene exhibit craniosynostosis, strongly supporting the proposition that the Pro148 -> His mutation is the cause of the disorder in humans (6 ). Overexpression/misexpression of the wild-type Msx2 gene in murine embryos can also produce craniosynostosis (6 ), a finding which when combined with the dominant nature of the mutation in humans argues that the mutation enhances the normal activity of Msx2. The molecular mechanism by which the Pro148 -> His substitution might cause this enhancement is the focus of this paper.
Extensive physical studies and domain swaps performed on several homeodomain proteins have demonstrated the importance of the N-terminal arm in minor groove DNA contacts (7 -10 ) and in interactions with auxiliary factors (11 ). It is thus plausible that the Pro148 -> His mutation could influence Msx2 target sequence recognition, the ability of Msx2 to interact with partner proteins, or both. A preliminary analysis suggested that there are no gross differences in the DNA binding properties of mutant and wild-type Msx2 proteins (12 ). Here, in a more detailed study, we demonstrate that bacterially expressed Pro148 -> His mutant Msx2 does in fact bind with higher affinity to several Msx2 DNA target sequences than does its wild-type counterpart. The basis of this increased affinity is a reduction in the dissociation rate of the Msx2-DNA complex. These data suggest a straightforward mechanism by which the Pro148 -> His mutation could lead to enhanced Msx2 activity and thus to mutant phenotypes in humans and mice.
We first asked whether there is a difference between the mutant and wild-type Msx2 proteins in affinity for a consensus Msx-class binding site. We designed a double stranded oligonucleotide containing the consensus Msx binding site, TAATTG (13 ,14 ). Using gel shift analysis, we measured the DNA binding affinity of both the wild-type and P148H Msx2 for this optimal Msx2 binding site. A binding site titration (15 ) was performed in which a varying amount of radiolabeled oligonucleotide was added to a series of binding reactions. The Msx2-DNA complexes were assayed by EMSA and quantitated in a phosphoimager. We estimated relative binding affinities of the mutant and wild-type Msx2 proteins by comparing the midpoints of the binding curves (15 ), an example of which is shown in Figure 1 .
We have addressed the underlying molecular cause of Boston-type craniosynostosis. We show that a mutation found exclusively in individuals affected with this disorder alters the DNA binding properties of the Msx2 homeoprotein. Although a preliminary study revealed no gross differences in DNA binding activity of mutant and wild-type Msx2 (12 ), our more extensive analysis has shown that the mutated (P148H) form of Msx2 interacts more avidly with consensus Msx2 binding sites than does its wild-type counterpart. This enhanced DNA binding affinity is caused largely if not entirely by enhanced stability of the Msx2-DNA complex. A binding site selection analysis revealed that the P148H mutation has no discernible effect on the sequence-specificity of Msx2 binding. This finding, together with our demonstration that the P148H mutation enhances the affinity of Msx2 for a consensus binding site, suggests that the P148H mutation has a generalized effect on Msx2 binding to different classes of binding sites.
Binding site selection studies, as well as physical analyses performed on several homeodomain proteins, have shown that the N-terminal arm has an important part in DNA binding (7 -9 ,16 ). Residues 3, 5 and 7 make base-specific contacts in the minor groove on the 5' side of the TAAT core sequence(7 ,8 ). Residue 6 contacts the sugar-phosphate backbone (7 ,9 ). Such contacts are at least in part responsible for some of the differences between homeodomain proteins in the DNA sequences to which they bind. Most significantly, mutations in residues 6 and 7 affect base preferences throughout the region contacted by the N-terminal arm, perhaps by influencing the overall conformation of the arm within the minor groove (10 ). Our results show that although the P148H mutation (corresponding to residue 7 of the homeodomain) does not influence Msx2 base preferences, it does increase the affinity of Msx2 for several target sequences, consistent with the well-documented involvement of the N-terminal arm in DNA binding. It is not obvious, however, why this mutation should have a positive rather than a negative effect on Msx2-target sequence interactions. The P148H substitution might, for example, reduce the flexibility of the arm and thus stabilize its minor groove contacts. It is also possible that the mutation affects charge density in the N-terminal arm. Protonation of the histidine in the local environment of the Msx2 protein-DNA complex would produce a positive charge in close proximity to the phosphate backbone and would thus presumably enhance DNA binding. We also point out that as residues in the arm do not function autonomously in sequence recognition, but act together with residues in helices I, II and III (16 ), the influence of the P148H mutation may extend beyond the N-terminal arm into other portions of the homeodomain.
The Boston craniosynostosis mutation behaves as an autosomal dominant in humans (3 ,4 ). Our finding that transgenic mice in which either the mutant or wild-type Msx2 gene is overexpressed also exhibit craniosynostosis is consistent with the possibility that the mutation acts via a dominant positive mechanism, i.e. that the mutation augments the normal function of Msx2. The data presented here on the enhancement of the DNA binding affinity of Msx2 are entirely consistent with this scenario. Although the magnitude of the enhancement in DNA binding is less than ten-fold, it may nevertheless be sufficient to explain the observed phenotypes. Measurements of the degree to which Msx2 is overexpressed in the developing cranial bones of Msx2 transgenic mice indicate a subtle effect, that two-fold or less overexpression is capable of causing sutural fusion (Liu, Y-H., Kundu, R., and Maxson, R., unpublished observations). Hence, it appears that the developing skull is highly sensitive to the level of Msx2 gene expression. A slight increase in the DNA binding affinity of the Msx2 protein may thus be sufficient to elicit craniosynostosis.
We stress, however, that a simple, linear model relating the abundance of Msx2 or its affinity for target sites to the fractional occupancy of such sites and thus to phenotype is likely to be an oversimplification. One complicating factor is the finding that the biological specificity of homeodomain proteins depends in part on auxiliary proteins with which they interact. For example, the exd-Ubx interaction enhances the DNA binding specificity of Ubx (17 -20 ), similarly, the interaction between the yeast [alpha]2 and MCM1 proteins modifies the activity and DNA binding properties of [alpha]2 (11 ). Such interactions depend on the N-terminal arms of the Ubx and [alpha]2 homeoproteins (18 ,19 ). If Msx2 function similarly involves protein-protein interactions mediated by the N-terminal arm, then the P148H mutation may, in addition to affecting DNA binding, perturb an interaction between Msx2 and a partner protein. Such an effect could influence Msx2 target sequence recognition indirectly, or might alter the ability of Msx2 to interact with the transcriptional machinery and thus regulate downstream genes.
In spite of these potential complexities, our data provide a framework in which to understand how a mutation in Msx2 can lead to the craniosynostosis phenotype. Further analysis of the molecular and developmental consequences of the P148H mutation is likely to illuminate not only the role of Msx2 in cranial development, but also general relationships between homeodomain structure, DNA target sequence recognition and interacting partner proteins.
Wild-type and P148H Msx2 cDNA were excised as a BamHI-EcoRI fragment from pBSK-Msx2 wild-type or pBSK-Msx2C -> A (P148H) (6 ). They were directionally cloned between the BamHI and EcoRI sites of pGEX-3X, which results in an in-frame fusion of the Msx2 proteins with glutathione-S-transferase (GST). Plasmids encoding the fusion proteins were transformed into the protease deficient bacterial strain BL21(DE3). GST-Msx2 proteins were expressed and purified as described (21 ).
Oligonucleotides were end-labeled with [[gamma]-32P]ATP using T4 polynucleotide kinase and opposite strands were allowed to anneal (22 ). Binding reactions were carried out by incubating 50 ng of purified GST fusion protein with 1 ng of probe in a buffer containing 10 mM Tris-HCl (pH 7.5), 50 mM potassium chloride, 0.05% Nonidet P-40, 0.1 [mu]g of bovine serum albumin per [mu]l, 5% (vol/vol) glycerol and 5 mM Dithiothreitol in 30 [mu]l reaction volume. Binding reactions were incubated for 15 min at room temperature, loaded without dye on 5% polyacrylamide, TBE gels, and electrophoresed at 8 V/cm for 2 h. Gels were dried and protein-DNA complexes were visualized and quantitated with a phosphoimager. For measurements of the dissociation rates of the Msx2-DNA complexes, complexes were formed as described above, and, after 15 min of incubation at room temperature, a 50-fold excess nonlabeled self-competitor was added. Aliquots of the binding reaction were withdrawn at various times and immediately loaded on a running polyacrylamide gel. Approximately 4 min elapsed between withdrawal of the sample from the binding reaction and entry into the gel.
Oligonucleotide selection was performed essentially as described by Abate and coworkers (13 ). Briefly, a DNA fragment containing 14 bp random sequence flanked on either side by 15 bases of nonrandom sequence [5'-AGACGGATCCATTGCA(N14)CTG- TAGGAATTCGGA-3'] was 32P-end-labeled and used in the gel shift assay as described above. Msx2-bound DNA was identified by autoradiography and extracted from the gel. The DNA was PCR-amplified, gel purified, end-labeled and used as a probe in a second round of gel retardation assays. A total of three rounds of selection were carried out. The resulting Msx2-bound DNA was cut with BamHI and EcoRI and cloned into BamHI-EcoRI digested pBluescript SK vector (Stratagene). Individual clones were sequenced by the dideoxy chain termination method (22 ).
We thank Dr Richard Maas and members of the Maxson laboratory for critical comments on this manuscript. This work was supported by NIH grants HD22416 and DE09165.
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*To whom correspondence should be addressed
+Present address: Howard Hughes Medical Institute, Brigham & Women's Hospital, 20 Shattuck St Boston, MA 02115, USA
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