GLOBULAR DOMAIN STRUCTURE AND FUNCTION OF RESTRICTION-LIKE-ENDONUCLEASE BEARING LONG INTERSPERSED NUCLEOTIDE ELEMENTS

Abstract

Long Interspersed Nucleotide Elements (LINEs) are a major group of eukaryotic transposable elements that have profoundly influenced and sculpted eukaryotic genome structure and function. LINEs replicate within the host genome, often to high copy number. Replication occurs through an RNA intermediate, which is integrated back into the host genome by target primed reverse transcription (TPRT). The element encoded protein is known to contain a restriction-like DNA endonuclease, a reverse transcriptase, and nucleic acid binding domains. However, the secondary and tertiary structure of these domains as well as the overall protein is poorly understood. The protein encoded by the R2 element from Bombyx mori (R2Bm) is expressible and purifiable and has thus facilitated much biochemical studies of the integration reaction. Using limited proteolysis and mass spectrometry, I studied globular domain structure of the R2Bm protein. It was discovered that the protein had two major globular domains: the zinc finger/Myb domain and the reverse transcriptase/linker/endonuclease superdomain. An easily proteolytically cleaved region between these two globular domains mapped to an area previously implicated in RNA binding. The large domain structure is similar to eukaryotic splicing factor protein Prp8's reverse transcriptase/linker/restriction endonuclease superdomain. An updated model of the reverse transcriptase domain of R2Bm protein was also generated and presented. The model was generated by protein threading and homology modeling algorithms. The model was tested by mapping the proteolytic cleavages back onto the model. Protein sequence alignments and structural overlays of the R2 reverse transcriptase and DNA endonuclease onto the splicing factor Prp8 indicate that the R2 protein and Prp8 likely shared a common ancestor. The structural and functional similarities in the linker region of both Prp8 and R2Bm are similarly discussed.