TBX22 missense mutations found in patients with X-linked cleft palate affect DNA binding, sumoylation, and transcriptional repression

Abstract

The T-box transcription factor TBX22 is essential for normal craniofacial development, as demonstrated by the finding of nonsense, frameshift, splice-site, or missense mutations in patients with X-linked cleft palate (CPX) and ankyloglossia. To better understand the function of TBX22, we studied 10 different naturally occurring missense mutations that are phenotypically equivalent to loss-of-function alleles. Since all missense mutations are located in the DNA-binding T-box domain, we first investigated the preferred recognition sequence for TBX22. Typical of T-box proteins, the resulting sequence is a palindrome based around near-perfect copies of AGGTGTGA. DNA-binding assays indicate that missense mutations at or near predicted contact points with the DNA backbone compromise stable DNA-protein interactions. We show that TBX22 functions as a transcriptional repressor and that TBX22 missense mutations result in impaired repression activity. No effect on nuclear localization of TBX22 was observed. We find that TBX22 is a target for the small ubiquitin-like modifier SUMO-1 and that this modification is required for TBX22 repressor activity. Although the site of SUMO attachment at the lysine at position 63 is upstream of the T-box domain, loss of SUMO-1 modification is consistently found in all pathogenic CPX missense mutations. This implies a general mechanism linking the loss of SUMO conjugation to the loss of TBX22 function. Orofacial clefts are well known for their complex etiology and variable penetrance, involving both genetic and environmental risk factors. The sumoylation process is also subject to and profoundly affected by similar environmental stresses. Thus, we suggest that SUMO modification may represent a common pathway that regulates normal craniofacial development and is involved in the pathogenesis of both Mendelian and idiopathic forms of orofacial clefting.

Figure 1.

Identification of the TBX22 preferred binding sequence. A, EMSA showing products of labeled double-stranded oligonucleotides and myc-tagged TBX22 protein after zero, two, and four rounds of selection. Lanes 1= free probe; lanes 2 = rabbit reticulocyte lysate; lanes 3 = rabbit reticulocyte lysate plus anti-myc antibody; lanes 4 = TBX22.myc; lanes 5 = TBX22.myc plus anti-myc antibody. B, Alignment of sequences from cloned and sequenced DNA fragments after four rounds of selection. The frequency of nucleotides found at each position is shown, along with the resulting consensus sequence that also represents the most common cloned sequence (7 of 16). Arrows highlight the half-sites comprising the imperfect inverted palindrome.

Figure 2.

Effect of missense mutations identified in a patient with CPX on DNA binding. A, Schematic diagram showing the location of missense mutations in TBX22. B, EMSA, to demonstrate the ability to shift or supershift the labeled TBX22 TBE probe by use of in vitro translated TBX22 proteins generated from wild-type (WT) or missense mutant constructs. FP = free probe; RRL = rabbit reticulocyte lysate control; minus sign (−) = protein as labeled; plus sign (+) = protein as labeled plus anti-myc antibody. To ensure equal loading in each lane, in vitro translated TBX22 proteins were immunoblotted with anti-myc antibody (top panel).

Figure 3.

Nuclear localization of wild-type and mutant TBX22 constructs. Constructs (pcDNA3.1.TBX22.V5/His) encoding wild-type (WT) or mutant TBX22 or empty pcDNA3.1-V5/His (Mock) were transfected into 293T cells. Cells were cultured for 48 h, were fixed, and were stained with DAPI and anti-V5/FITC.

Figure 4.

Identification of TBX22 promoter sequences. A, Schematic diagram of the putative promoters hP0 and hP1 that generate different transcripts. These were initially identified by bioinformatic analysis of genomic and EST sequence databases and were confirmed experimentally by RT-PCR analysis. B, pGL3-hP0 (P0) and pGL3-hP1 (P1) reporter constructs, transfected into 293T cells together with control pGL3 (white bars indicate sense; black bars indicate antisense). Minus sign (−) = empty vector. C, Relative promoter activity, determined after truncated pGL3-hP0 constructs were transfected into 293T cells.

Figure 5.

TBX22, which acts as a transcriptional repressor. A, RT-PCR performed using primers in TBX22 exons 5–8, to show endogenous expression in human cell lines (upper panel), and in β-ACTIN, to confirm RNA integrity and loading (lower panel). Plus signs (+) and minus signs (−) indicate reverse transcriptase–positive and –negative treated samples, respectively. B, Cotransfection of pGL3-hP0 with increasing amounts (2.5, 10, and 25 ng) of pcDNA3.1.TBX22.V5/His expression construct, performed in 293T cells. WT = wild type. C, 293T cells, cotransfected with a luciferase reporter construct containing GAL4 and LexA binding sites. The addition of LexA-VP16 to the transfection results in activation of the basic promoter. Addition of increasing amounts (1 and 10 ng) of full-length GAL4-TBX22, N-terminal (1–101), and T-box (100–285) constructs demonstrate dose-dependent repression, whereas the C-terminal (285-520) fusion construct demonstrates inactivity or slight activation. D, Repression of pGL3-hP0 by wild-type TBX22 was compared with that of natural missense mutations found in patients with CPX. Different experiments were compared by normalizing to the basal promoter activity of pGL3-hP0 (100%). Dotted lines represent maximal and minimal activity. Relative promoter activity was determined by normalizing the luciferase values to the internal control cytomegalovirus-Renilla, and each bar is representative of an experiment done in quadruplicate and on at least three separate occasions.

Figure 6.

Posttranslational modification of TBX22 by SUMO-1. A, Western-blot analysis of protein extracts from COS-1 cells transfected with pCDNA3.1.TBX22-V5/His only and with wild-type SUMO1-GG-HSTV or inactive SUMO1-ΔGG mutant. B, Western blots showing coimmunoprecipitation of TBX22.V5 and SUMO-1 wild-type or mutant after transfection into COS-1 cells. The interaction of TBX22 with wild-type SUMO-1 can be visualized with both anti–SUMO-1 and anti-V5 antibodies. M = molecular-weight marker.

Figure 7.

Effect of SUMO-1 conjugation on TBX22 activity. A, Sequence alignment of human and mouse TBX22, highlighting the position of the three SUMO consensus attachment motifs (ΨKXE/D) found in the human sequence. Asterisks (*) mark the lysine residues at putative SUMO attachment sites K54, K63, and K271. Western-blot analysis with anti-V5 antibody shows sumoylation of wild-type (WT), K54R, and K271R mutant constructs. K63R is not modified even when SUMO is overexpressed. B, Effect of lysine→arginine mutations in TBX22 on hP0 promoter activity. C, EMSA showing effect of K54R, K63R, and K271R mutations on DNA binding compared with the wild type. FP = free probe; RRL = rabbit reticulocyte lysate negative control; minus sign (−) = without addition of anti-V5; plus sign (+) = with addition of anti-V5.

Figure 8.

Profound affect of missense mutations on TBX22–SUMO-1 conjugation. A, Effect of cotransfecting SENP1 and SENP2 on hP0 promoter activity repression by TBX22. WT = wildtype. B, Western blots with anti-V5 antibody, showing cotransfections of TBX22-V5 constructs with increasing concentrations of SENP1 and SENP2 (top panel). The middle panel confirms the expression of the SENP1 and SENP2 proteins by use of an anti-FLAG antibody. The third panel shows a decrease of total SUMO-1 conjugates and a rise in free SUMO-1 levels with increased SENP concentration. A control for equal loading was performed using anti–β-actin antibody (bottom panel). C, Western blotting of transfected TBX22-V5 proteins containing natural missense mutations with anti-V5 antibody (top panel). Approximately even levels of endogenous SUMO-1 conjugates are seen in each lane (bottom panel).