DNA target site recognition by the Ll.LtrB group II intron RNP
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Mobile group II introns are retroelements that site-specifically insert into DNA target sequences. The group II intron mobility pathway is mediated by a ribonucleoprotein particle (RNP) composed of excised intron RNA and an intron-encoded protein (IEP). The intron lariat inserts at a specific DNA target sequence and is then reverse transcribed by the IEP. Both the intron RNA and IEP are required for DNA target site recognition. I have identified the contact sites within the IEP responsible for recognition of two key positions in the DNA target, T+5 and T-23. IEP recognition of T+5 in the 3'-exon is required for endonuclease cleavage of the bottom-strand of the DNA target site, which generates a primer used for initiation of reverse transcription of the intron. The T+5 base is contacted by G498 in the LtrA DNA-binding domain and nearby residues, particularly K499, potentially bolster this interaction. Recognition of T-23 in the distal 5'-exon is required for initial recognition of the DNA target site by the RNP. The T533 side-chain contacts the T-23 base and the L534 side-chain may also contribute to recognition through hydrophobic interactions with the C5 methyl group. A mutant, L534H, that switches target site specificity to T-23G has been characterized. In order for the RNP to make these and other contacts in the 5'- and 3'-exons simultaneously, the DNA must be bent. I have dissected the role of DNA bending in the intron mobility pathway and found that the DNA is bent at two progressively larger angles as the reaction proceeds. The predominant bend angle at earlier time points places the bottom-strand DNA cleavage site at the protein endonuclease active site. The predominant bend angle of later time points places the cleaved DNA site at the RT domain active site for initiation of reverse transcription of intron cDNA. Finally, in a practical application of group II intron mobility, I have used reprogrammed group II introns ("targetrons") to target two genes in Bacillus subtilis to demonstrate the suitability of targetron technology for gene targeting in the Gram-positive Bacillus genus.