DNA-Binding Specificity of the IDI-4 Basic Leucine Zipper Factor of Podospora anserina Defined by Systematic Evolution of Ligands by Exponential Enrichment (SELEX)

Abstract

Heterokaryon incompatibility is a cell destruction process that occurs when fungal cells of unlike genotype fuse. In Podospora anserina, autophagy is engaged during cell death by incompatibility and a number of genes are induced at the transcriptional level. These genes are termed idi (induced during incompatibility) genes. Among these is idi-4, a gene encoding a basic leucine zipper (bZIP) factor. IDI-4 displays similarity to the GCN4/cross-pathway control (CPC) factors that control gene expression in response to amino acid starvation in fungi. The overexpression of idi-4 triggers autophagy, leads to cell death, and also increases the expression of a number of idi genes, in particular idi-7, a gene involved in autophagy. Herein, we determined the in vitro target sequence of IDI-4. We have purified the recombinant IDI-4 bZIP domain and show that this 83-amino-acid-long peptide dimerizes in vitro and adopts an alpha-helical fold. We have then used a systematic evolution of ligands by exponential enrichment procedure to identify the sequence bound by the IDI-4 bZIP domain. The IDI-4 binding site consensus sequence corresponds to the ATGANTCAT pseudopalindrome. IDI-4 binding sites are present in the promoter region of the idi-7 gene, and the bZIP IDI-4 peptide binds to the idi-7 promoter in vitro. The identified IDI-4 consensus binding sequence is very similar to the GCN4/CPC binding site, raising the possibility of an interplay and/or partial functional redundancy between IDI-4 and CPC-type bZIP factors in fungi.