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Homing endonucleases are often grouped into four families based on distinct sequence motifs. One of these families is known as the His-Cys box homing endonucleases and contains two clusters of conserved histidine and cysteine residues over a central 100 amino acid region. At last count, 23 members of this family had been identified. The open reading frames (ORFs) of these proteins are contained within mobile group I introns found in nuclear rDNA genes of several protists. The nuclear location of these introns and ORFs is currently unique among the homing endonuclease families and poses an intriguing puzzle regarding their expression from non-coding rRNA transcripts. The best-studied member of the His-Cys box homing endonucleases is I-PpoI from the myxomycete Physarum polycephalum . Following an introduction to all of the known members of the His-Cys box endonuclease family, much of the following chapter will outline the extensive characterization of I-PpoI structure and function. Although our understanding of how I-PpoI is expressed in cells is still not fully complete, the means by which I-PpoI specifically recognizes a single cleavage site in the host genome to mediate homing of its host intron is widely accepted. Details of DNA recognition and the catalytic mechanism of nucleolytic cleavage have been ascertained from both in vivo and in vitro activity assays as well as from extensive X-ray crystallographic structural analyses of the enzyme bound to its DNA substrate.

Homing endonucleases are a class of invasive genetic elements that use several elegant solutions to ensure their survival in natural populations. Like all successful mobile entities, homing endonucleases must either reduce the deleterious effects of insertion within essential genes of host genomes or be lost. Many homing endonuclease genes have solved this problem by colonizing self-splicing group I introns. This association makes homing endonuclease genes phenotypically “silent” since they are spliced out and thus absent from the mature mRNA of the invaded gene. Through this union, homing endonucleases and introns have co-evolved into a “hybrid” mobile element providing the introns with a mechanism to propagate themselves in a population. Remarkably, in some cases within fungal mitochondrial genomes, homing endonucleases have adapted to facilitate splicing of their encoding introns and contribute to the host’s regulation of the invaded gene. This novel adaptation, termed maturase activity, has likely served to ensure their fixture in mitochondrial and, perhaps, other genomes. In this chapter, we will review what is known concerning the mechanism of group I intron-encoded protein-assisted splicing. In addition, we will summarize new studies of both mobility and maturase functions that have resulted in a better understanding of how a single polypeptide carries out diverse and unrelated activities. Principles derived from maturase systems are likely to apply to numerous other multi-functional proteins that participate in diverse metabolic pathways.