Homing into the origin of the AP2 DNA binding domain

The AP2 DNA binding domain was thought to be plant specific because of its presence in plant, but not animal, transcriptional regulators, particularly members of the AP2/ERF family. Two recent studies have identified the AP2 domain in bacteria, bacteriophage and a ciliate as part of proteins that also encode site-specific endonucleases. The association of AP2 with an enzyme known to catalyze its own movement within populations and between species explains the unusual distribution of AP2 and, as such, adds to a growing list of phenomena where mobile DNA has promoted evolutionary novelty.

Introduction

The cloning of the Arabidopsis APETALA2 (AP2) gene led to the surprising finding that it did not contain a MADS domain like that in previously isolated floral regulators. Instead, the AP2 protein harbored two copies of a 68 amino acid sequence that came to be known as the AP2 domain [1]. Soon after, this domain was recognized in four tobacco proteins where it was shown to be required to bind the so-called GCC box in the promoters of genes that encode ethylene-inducible pathogenesis-related proteins [2]. Ever since these initial discoveries, the number of AP2-containing proteins has increased dramatically, with almost 150 in the Arabidopsis genome alone and hundreds more in other flowering plants. However, until the recent publication of papers by Kathleen Karrer and colleagues [3] and Sarah Hake and colleagues [4], there had been no reports of an AP2 ‘sighting’ outside of the plant kingdom. This contrasts dramatically with most other DNA binding domains (e.g. bHLH, MADS, homeo and zinc fingers), which are found in both plant and animal genomes.

This story begins with the discovery by Wuitschick et al. [3] that three members of a family of mobile elements in the ciliate Tetrahymena thermophila contain insertions that encode bifunctional proteins with a site-specific (homing) endonuclease domain and an AP2 domain. Like other ciliates, T. thermophila has two nuclei: a silent germline micronucleus and a transcriptionally active (somatic) macronucleus. Open reading frames (ORFs) in the micronucleus are interrupted by thousands of transposable elements of different types. In a remarkable series of programmed genomic rearrangements, the development of the macronucleus from a mitotic product of the micronucleus is accompanied by the precise removal of these insertions, called internal eliminated sequences (IESs). As part of their analysis of IESs in Tetrahymena, Wuitschick et al. 3, 5 noted that three members of one IES families, called Tlr (Tetrahymena long repeat), contain distinct but related genes that encode putative homing endonuclease and AP2 domains.

Shortly after this study was published, a paper from Hake's laboratory [4] reported the results of an extensive computer-assisted search for AP2 domain homologs that are outside the plant kingdom. In addition to identifying the three proteins from T. thermophila, they detected AP2 homologs in the cyanobacterium Trichodesmium erythraeum and in the viruses Enterbacteria phage RB49 and Bacteriophage Felix 01. Enrico Magnani et al. [4] went on to demonstrate that the cyanobacterium AP2 domain binds preferentially to DNA substrates with poly(G)/poly(C) stretches. Binding sites of many plant AP2 domains are also rich in G and C residues, indicating that this domain has been functionally conserved. Whether in ciliates, bacteria or viruses, the AP2 domains in nonplant species are encoded by genes that also encode homing endonucleases.