Comparison of TFII-I gene family members deleted in Williams-Beuren syndrome

Abstract

Williams-Beuren syndrome (WBS) is a neurological disorder resulting from a microdeletion, typically 1.5 megabases in size, at 7q11.23. Atypical patients implicate genes at the telomeric end of this multigene deletion as the main candidates for the pathology of WBS in particular the unequal cognitive profile associated with the condition. We recently identified a gene (GTF2IRD2) that shares homology with other members of a unique family of transcription factors (TFII-I family), which reside in the critical telomeric region. Using bioinformatics tools this study focuses on the detailed assessment of this gene family, concentrating on their characteristic structural components such as the leucine zipper (LZ) and I-repeat elements, in an attempt to identify features that could aid functional predictions. Phylogenetic analysis identified distinct I-repeat clades shared between family members. Linking functional data to one such clade has implicated them in DNA binding. The identification of PEST, synergy control motifs, and sumoylation sites common to all family members suggest a shared mechanism regulating the stability and transcriptional activity of these factors. In addition, the identification/isolation of short truncated isoforms for each TFII-I family member implies a mode of self-regulation. The exceptionally high identity shared between GTF2I and GTF2IRD2, suggests that heterodimers as well as homodimers are possible, and indicates overlapping functions between their respective short isoforms. Such cross-reactivity between GTF2I and GTF2IRD2 short isoforms might have been the evolutionary driving force for the 7q11.23 chromosomal rearrangement not present in the syntenic region in mice.

Figure 1.

(A) Schematical representation of TFII-I family members. LZ (dark gray) and I-repeat structural elements are shown. I-repeats are patterned in accordance to the clade groupings identified through phylogenetic analysis, (see below) and the length of each protein is given. (B) Phylogeny of I-repeats. Neighbor-joining tree of I-repeats found in the three members of the TFII-I family; GTF2I, GTF2IRD1, and GTF2IRD2. Amino acid sequences for the full-length proteins for both human and mouse (lowercase) I-repeats are detailed. Bootstrap values calculated for 1000 replicates are shown for clades I and II, and the scale bar indicates distance of divergence.

Figure 2.

Multiple alignment of leucine zipper domains found in the three members of the human TFII-I family. Leucine zipper sequences are aligned with the heptad positions a–g, labeled above. Residues at key heptad positions a, d, e, or g (bold) have their conserved physiochemical properties below the alignment (ψ, hydrophobic; –, negatively charged residues) and those that are different to their TFII-I family counterparts are highlighted.

Figure 3.

Predicted I-repeat structure. (A) Multiple alignment of I-repeats from GTF2I, GTF2IRD1, and GTF2IRD2. Individual I-repeats (grouped in clades) are numbered according to their location from the N terminus of the protein. The HLH consensus (Murre et al. 1989) is manually aligned against the I-repeat consensus: Conserved residues are in bold; partially conserved residues (P,G) in the putative loop region are highlighted gray; ψ denotes conserved hydrophobic positions. The HLH consensus described in Roy et al. (1997) is aligned against the appropriate residues (Φ and Ω are not defined in the original text). The six basic residues required for GTF2I Inr binding are underlined, and putative basic residues required for GTF2IRD1 I-4 DNA binding are boxed. (B) Comparison of the putative HLH structure for GTF2I I-R5 against a PSI-PRED secondary structure prediction of the protein (typical of all I-repeats). The residues predicted with helical (cylinder) or β-strand structures (arrow) are highlighted in gray, with random coil sequence represented by a straight line in the cartoon.

Figure 4.

(A) Pairwise alignment of GTF2I (NP_127492) and Gtf2i (AAK49788) residues 1–389 and 804–899. Tcr2 site (boxed), Tcr3 site (boxed and italicized text), and the ERK binding site identified in GTF2I (italicized and underlined). (B) Pairwise alignment of GTF2IRD1 (AAF19786) and Gtf2ird1 (AAF78367) residues 396–595. Ccr2 site (boxed), Ccr3 site (boxed and italicized text). (C) Pairwise alignment of GTF2IRD2 (NP_775808) and Gtf2ird2 (AAG41674) residues 1–300. Mcr3 site (boxed and italicized text). Common annotations: I-repeats (underlined), predicted PEST sequence (bold), sumoylation sites of high probability (dark gray), and synergy control motifs (dark gray sumoylation site flanked by light gray sequence that includes a proline).

Figure 5.

Schematic diagrams of GTF2I/Gtf2i, GTF2IRD2/Gtf2ird2, full-length, and short isoforms. Exons are represented as rectangles. Exons coding for leucine zipper are shaded black; I-repeats are shaded dark gray, with the respective annotated I-repeat number; and GTF2IRD2 charlie8 exon 16 is in light gray. The position of the new termination codon is indicated in the short isoforms. Genbank accession numbers are indicated.