DNA-Binding Specificity of the PAR Basic Leucine Zipper Protein VBP Partially Overlaps Those of the C/EBP and CREB/ATF Families and Is Influenced by Domains That Flank the Core Basic Region

Abstract

The PAR subfamily of basic leucine zipper (bZIP) factors comprises three proteins (VBP/TEF, DBP, and HLF) that have conserved basic regions flanked by proline-and acidic-amino-acid-rich (PAR) domains and functionally compatible leucine zipper dimerization domains. We show that VBP preferentially binds to sequences that consist of abutted GTAAY half-sites (which we refer to as PAR sites) as well as to sequences that contain either a C/EBP half-site (GCAAT) or a CREB/ATF half-site (GTCAT) in place of one of the PAR half-sites. Since the sequences that we describe as PAR sites and PAR-CREB/ATF chimeric sites, respectively, were both previously described as high-affinity binding sites for the E4BP4 transcriptional repressor, we infer that these sequences may be targets for positive and negative regulation. Similarly, since the sequences that we describe as PAR-C/EBP and PAR-CREB/ATF chimeric sites are known to be high-affinity binding sites for C/EBP and CREB/ATF factors, respectively, we infer that these sites may each be targets for multiple subfamilies of bZIP factors. To gain insights regarding the molecular basis for the binding-site specificity of PAR factors, we also carried out an extensive mutational analysis of VBP. By substituting five amino acid residues that differ between the Drosophila giant bZIP factor and the vertebrate PAR bZIP factors, we show that the fork region, which bridges the basic and leucine zipper domains, contributes to half-site sequence specificity. In addition, we report that at least two domains amino terminal to the core basic region are required for VBP to bind to the full spectrum of PAR target sites. Thus, whereas direct base contacts may be restricted to basic-region residues (as indicated by GCN4-DNA crystal structures), several other domains also influence the DNA-binding specificity of PAR bZIP proteins.

CCAAT/Enhancer-Binding Protein Phosphorylation Biases Cortical Precursors to Generate Neurons Rather Than AstrocytesIn Vivo

“…Alternatively, the C/EBPs might promote neurogenesis by sequestering activating transcription factor 5 (ATF5), another transcription factor of the leucine zipper family that maintains neural precursors in an undifferentiated state (Angelastro et al, 2003(Angelastro et al, , 2005. Previous work has shown that C/EBPs and ATFs can heterodimerize (Shuman et al, 1997) and that the heterodimers bind to different DNA binding sites than do either ATF or C/EBP homodimers (Haas et al, 1995). Thus, the relative levels and activation state of ATF5 versus C/EBPs may well determine whether or when a precursor differentiates into a neuron.…”

Molecular Cloning and Characterization of NF-IL3A, a Transcriptional Activator of the Human Interleukin-3 Promoter

“…1; the basic amino acid region and the leucine zipper region are indicated. The basic amino acid region of NF-IL3A appears to be more related to members of the proline-and acidic amino acid-rich (PAR) family of bZIP transcription factors, such as albumin promoter D-box-binding protein (DBP), thyrotroph embryonic factor (TEF), and hepatic leukemia factor (HLF), than to members of the AP-1 family (11,15,16,26).…”

The CES-2-related transcription factor E4BP4 is an intrinsic regulator of motoneuron growth and survival

“…Although their sequence similarity is distant, they share a consensus DNA-binding site (Cowell et al, 1992;Drolet et al, 1991;Falvey et al, 1995;Fonjallaz et al, 1996;Haas et al, 1995;Hunger et al, 1992). One of these, E4BP4 (also known as NFIL3), can act in different contexts as a transcriptional repressor or activator (Cowell et al, 1992;Lai and Ting, 1999;Zhang et al, 1995).…”